Mercurial > repos > galaxyp > msi_qualitycontrol

annotate msi_qualitycontrol.xml @ 16:f56166082222 draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
author galaxyp
date Wed, 22 Aug 2018 13:34:45 -0400
parents 898dec99d9fc
children
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16
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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.7">
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2 <description>
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3 mass spectrometry imaging QC
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4 </description>
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5 <requirements>
8
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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9 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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10 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
10
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11 <requirement type="package" version="0.5.0">r-scales</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 #if $infile.ext == 'imzml'
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16 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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17 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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18 #elif $infile.ext == 'analyze75'
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19 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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20 ln -s '${infile.extra_files_path}/img' infile.img &&
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21 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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22 #else
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23 ln -s '$infile' infile.RData &&
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24 #end if
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25 cat '${cardinal_qualitycontrol_script}' &&
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26 Rscript '${cardinal_qualitycontrol_script}'
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
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31
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32 ################################# load libraries and read file #################
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33
0
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34 library(Cardinal)
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35 library(ggplot2)
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36 library(RColorBrewer)
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37 library(gridExtra)
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38 library(KernSmooth)
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39 library(scales)
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41
0
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42 #if $infile.ext == 'imzml'
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43 #if str($processed_cond.processed_file) == "processed":
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44 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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45 #else
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46 msidata <- readImzML('infile')
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47 #end if
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48 #elif $infile.ext == 'analyze75'
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49 msidata = readAnalyze('infile')
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50 #else
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51 loadRData <- function(fileName){
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52 load(fileName)
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53 get(ls()[ls() != "fileName"])
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54 }
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55 msidata = loadRData('infile.RData')
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56 #end if
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57
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58 ## remove duplicated coordinates
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59 print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))
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60 msidata <- msidata[,!duplicated(coord(msidata))]
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61
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62 ## create full matrix to make processed imzML files compatible with segmentation and other steps
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63 iData(msidata) <- iData(msidata)[]
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64
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65 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
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66
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67 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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68
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69 ## read and extract x,y,annotation information
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70 input_tabular = read.delim("$tabular_annotation.annotation_file", header = TRUE, stringsAsFactors = FALSE)
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71 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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72 annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
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73 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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74
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75 ## merge with coordinate information of msidata
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76 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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77 colnames(msidata_coordinates)[3] = "pixel_index"
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78 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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79 merged_annotation[is.na(merged_annotation)] = "NA"
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80 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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81 msidata\$annotation = as.factor(merged_annotation[,4])
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82
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83 #end if
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84
0
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85 ###################################### file properties in numbers ######################
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86
9
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87 ## Number of features (m/z)
0
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88 maxfeatures = length(features(msidata))
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89 ## Range m/z
0
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90 minmz = round(min(mz(msidata)), digits=2)
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91 maxmz = round(max(mz(msidata)), digits=2)
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92 ## Number of spectra (pixels)
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93 pixelcount = length(pixels(msidata))
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94 ## Range x coordinates
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95 minimumx = min(coord(msidata)[,1])
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96 maximumx = max(coord(msidata)[,1])
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97 ## Range y coordinates
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98 minimumy = min(coord(msidata)[,2])
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99 maximumy = max(coord(msidata)[,2])
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100 ## Range of intensities
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101 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
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102 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
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103 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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104 ## Number of intensities > 0
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105 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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106 ## Spectra multiplied with m/z (potential number of peaks)
0
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107 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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108 ## Percentage of intensities > 0
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109 percpeaks = round(npeaks/numpeaks*100, digits=2)
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110 ## Number of empty TICs
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111 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
0
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112 NumemptyTIC = sum(TICs == 0)
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113 ## Median TIC
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114 medTIC = round(median(TICs), digits=2)
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115 ## Median peaks per spectrum
13
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116 medpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE)
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117 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))
0
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118
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119 ## Processing informations
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120 processinginfo = processingData(msidata)
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121 centroidedinfo = processinginfo@centroided
0
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122
9
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123 ## if TRUE write processinginfo if FALSE write FALSE
0
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124
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125 ## normalization
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126 if (length(processinginfo@normalization) == 0) {
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127 normalizationinfo='FALSE'
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128 } else {
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129 normalizationinfo=processinginfo@normalization
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130 }
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131 ## smoothing
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132 if (length(processinginfo@smoothing) == 0) {
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133 smoothinginfo='FALSE'
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134 } else {
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135 smoothinginfo=processinginfo@smoothing
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136 }
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137 ## baseline
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138 if (length(processinginfo@baselineReduction) == 0) {
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139 baselinereductioninfo='FALSE'
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140 } else {
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141 baselinereductioninfo=processinginfo@baselineReduction
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142 }
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143 ## peak picking
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144 if (length(processinginfo@peakPicking) == 0) {
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145 peakpickinginfo='FALSE'
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146 } else {
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147 peakpickinginfo=processinginfo@peakPicking
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148 }
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149
9
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150 ############## Read and filter tabular file with m/z ###########################
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151
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152 ### reading calibrant file:
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153
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154 #if $calibrant_file:
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155
4
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156 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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157 if (ncol(calibrant_list) == 1)
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158 {calibrant_list = cbind(calibrant_list, calibrant_list)} ## if there is just one column dublicate it to have a names column
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159
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160 ### calculate how many input calibrant m/z are valid:
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161
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162 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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163 number_calibrants_in = length(calibrant_list[,1])
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164 number_calibrants_valid = length(inputcalibrants[,1])
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165
4
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166 #else
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167
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168 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
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169 number_calibrants_in = 0
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170 number_calibrants_valid = 0
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171
4
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172 #end if
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173
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174 ## rename input dataframe and extract m/z
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175 colnames(inputcalibrants) = c("m/z", "name")
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176 inputcalibrantmasses = inputcalibrants[,1]
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177
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178
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179 ######################################## PDF #############################################
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180 ##########################################################################################
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181 ##########################################################################################
0
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182
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183 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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184 plot(0,type='n',axes=FALSE,ann=FALSE)
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185
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186 ## if no filename is given, name of file in Galaxy history is used
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187
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188 #if not $filename:
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189 #set $filename = $infile.display_name
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190 #end if
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191
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192 title(main=paste("$filename"))
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193
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194 ################# I) file properties in numbers ################################
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195 ################################################################################
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196 print("properties in numbers")
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197
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198 properties = c("Number of m/z features",
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199 "Range of m/z values",
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200 "Number of pixels",
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201 "Range of x coordinates",
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202 "Range of y coordinates",
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203 "Range of intensities",
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204 "Median of intensities",
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205 "Intensities > 0",
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206 "Number of empty spectra",
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207 "Median TIC",
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208 "Median # peaks per spectrum",
0
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209 "Normalization",
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210 "Smoothing",
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211 "Baseline reduction",
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212 "Peak picking",
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213 "Centroided",
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214 paste0("calibrants (#valid/#input) in \n", "$calibrant_file.display_name"))
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215
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216 values = c(paste0(maxfeatures),
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217 paste0(minmz, " - ", maxmz),
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218 paste0(pixelcount),
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219 paste0(minimumx, " - ", maximumx),
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220 paste0(minimumy, " - ", maximumy),
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221 paste0(minint, " - ", maxint),
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222 paste0(medint),
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223 paste0(percpeaks, " %"),
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224 paste0(NumemptyTIC),
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225 paste0(medTIC),
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226 paste0(medpeaks),
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227 paste0(normalizationinfo),
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228 paste0(smoothinginfo),
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229 paste0(baselinereductioninfo),
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230 paste0(peakpickinginfo),
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231 paste0(centroidedinfo),
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232 paste0(number_calibrants_valid, " / ", number_calibrants_in))
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233
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234 property_df = data.frame(properties, values)
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235
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236 grid.table(property_df, rows= NULL)
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237
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238 ####################### II) x-y images #######################################
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239 ##############################################################################
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240 print("x-y images")
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241
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242 ## only do plots for file with intensity peaks
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243 if (npeaks > 0){
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244 ## function for density plots
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245 plot_colorByDensity = function(x1,x2,
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246 ylim=c(min(x2),max(x2)),
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247 xlim=c(min(x1),max(x1)),
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248 xlab="",ylab="",main=""){
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249 df = data.frame(x1,x2)
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250 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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251 df\$dens = col2rgb(x)[1,] + 1L
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252 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
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253 df\$col = cols[df\$dens]
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254 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
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255 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
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256
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257 ## start list for optional spectrum values output
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258 spectrum_list = list()
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259 list_count = 1
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260
9
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261 ################### 0) overview for combined data ###########################
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262
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263 ### only for previously combined data, same plot as in combine QC pdf
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264
14
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265 if (!is.null(levels(msidata\$annotation))){
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266 number_combined = length(levels(msidata\$annotation))
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267
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268 ## the more annotation groups a file has the smaller will be the legend
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269 if (number_combined<20){
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270 legend_size = 10
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271 cex_boxplot = 1
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272 }else if (number_combined>20 && number_combined<40){
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273 legend_size = 9
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274 cex_boxplot = 0.8
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275 }else if (number_combined>40 && number_combined<60){
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276 legend_size = 8
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277 cex_boxplot = 0.6
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278 }else if (number_combined>60 && number_combined<100){
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279 legend_size = 7
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280 cex_boxplot = 0.5
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281 }else{
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282 legend_size = 6
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283 cex_boxplot = 0.3
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284 }
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285
14
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286 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
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287 colnames(position_df)[3] = annotation_name
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288
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289 ## append list for optional tabular output with spectrum values
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290 spectrum_list[[list_count]] = position_df
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291 list_count = list_count+1
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292
15
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293 colnames(position_df)[3] = "annotation"
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294
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295 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
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296 geom_tile() +
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297 coord_fixed()+
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298 ggtitle("Spatial orientation of pixel annotations")+
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299 theme_bw()+
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300 theme(plot.title = element_text(hjust = 0.5))+
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301 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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302 theme(legend.position="bottom",legend.direction="vertical")+
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303 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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304 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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305
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306 print(combine_plot)
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307
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308 ### order pixels according to annotation - this gives a new pixel/spectra index order according to the annotation groups
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309 pixel_name_df = data.frame(pixels(msidata), msidata\$annotation)
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310 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
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311
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312 pixel_name_df_ordered = pixel_name_df[order(pixel_name_df\$pixel_name),]
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313 pixel_name_df_ordered\$annotated_order = 1:ncol(msidata)
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314 last_pixel = aggregate(annotated_order~pixel_name, data = pixel_name_df_ordered, max)
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315
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316 pixel_vector = last_pixel[,2]
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317 abline_vector = pixel_vector[1:number_combined-1]
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318 print(abline_vector)
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319 }
0
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320
9
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321 ################### 1) Pixel order image ###################################
2
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322
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323 pixelnumber = 1:pixelcount
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324 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
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325 gg_title = "Pixel order"
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326
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327 ## order pixels according to annotation groups if annotations are provided
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328 if (!is.null(levels(msidata\$annotation))){
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329 pixelxyarray = pixelxyarray[match(pixel_name_df_ordered\$pixel_number, pixelxyarray\$pixelnumber),]
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330 pixelxyarray\$pixelnumber = 1:ncol(msidata)
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331 gg_title = "Pixel ordered for annotation groups"
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332 }
0
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333
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334 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+
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335 geom_tile() + coord_fixed()+
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336 ggtitle(gg_title) + theme_bw()+
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337 theme(plot.title = element_text(hjust = 0.5))+
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338 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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339 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
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340 space = "Lab", na.value = "black", name = "Pixel\nnumber"))
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341
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342 ################ 2) Number of calibrants per spectrum ######################
0
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343
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344 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
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345 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
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346
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347 ## plot only possible when there is at least one valid calibrant
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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348 if (length(inputcalibrantmasses) != 0){
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349
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350 ## calculate plusminus values in m/z for each calibrant
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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351 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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352
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353 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
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354
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355 for (mass in 1:length(inputcalibrantmasses)){
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356
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357 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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358
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359 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){
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360
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361 ## intensity of all m/z > 0
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362 intensity_sum = colSums(spectra(filtered_data)[], na.rm=TRUE) > 0
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363
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364 }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data)[], na.rm=TRUE) > 0){
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365
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366 ## intensity of only m/z > 0
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367 intensity_sum = spectra(filtered_data)[] > 0
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368
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369 }else{
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370
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diff changeset
371 intensity_sum = rep(FALSE, ncol(filtered_data))}
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372
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373 ## for each pixel add sum of intensities > 0 in the given m/z range
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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374 pixelmatrix = rbind(pixelmatrix, intensity_sum)
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375 }
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diff changeset
376
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377 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
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378 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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379 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
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380 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
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381
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382 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+
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383 geom_tile() + coord_fixed() +
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384 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) +
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diff changeset
385 theme_bw() +
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diff changeset
386 theme(plot.title = element_text(hjust = 0.5))+
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diff changeset
387 theme(text=element_text(family="ArialMT", face="bold", size=12))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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388 scale_fill_manual(values = mycolours[1:length(countvector)],
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389 na.value = "black", name = "# calibrants"))
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diff changeset
390
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391 ## append list for optional tabular output with spectrum values
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diff changeset
392 colnames(countdf)[3] = "Number of Calibrants"
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
393 spectrum_list[[list_count]] = countdf
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
394 list_count = list_count+1
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395
9
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396 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
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397
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398 ########################## 3) fold change image ###########################
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diff changeset
399
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diff changeset
400 #if $calibrantratio:
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401 #for $foldchanges in $calibrantratio:
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402 mass1 = $foldchanges.mass1
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403 mass2 = $foldchanges.mass2
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diff changeset
404 distance = $foldchanges.distance
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405
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406 ### if user did not write a label use input m/z as label
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407 #if not str($foldchanges.filenameratioplot).strip():
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408 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
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diff changeset
409 #else:
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diff changeset
410 #set $label = $foldchanges.filenameratioplot
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diff changeset
411 #end if
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diff changeset
412
9
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diff changeset
413 ### filter msidata for given m/z range (for both input m/z)
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414 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,]
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diff changeset
415 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,]
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416
9
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417 ### find m/z in the two given ranges with the highest mean intensity
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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418 ### this two m/z will be used to calculate the fold change (red line in plot)
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419 maxmassrow1 = rowMeans(spectra(filtered_data1), na.rm=TRUE)
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420 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)]
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421 maxmassrow2 = rowMeans(spectra(filtered_data2), na.rm=TRUE)
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diff changeset
422 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)]
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423
9
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424 ### plot legend: chosen value in blue, distance in blue, max m/z in red
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diff changeset
425 ### m/z range for each plot (fixed range of 5 Da)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
426 ### xlim does not work because it does not adjust for the max. intensities within the range
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
427 mzdown1 = features(msidata, mz = mass1-2)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
428 mzup1 = features(msidata, mz = mass1+3)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
429 mzdown2 = features(msidata, mz = mass2-2)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
430 mzup2 = features(msidata, mz = mass2+3)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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431
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
432 ### plot for first m/z
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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433 par(mfrow=c(2,1), oma=c(0,0,2,0))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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434 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
435 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,6,3))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
436 abline(v=maxmass1, col="red", lty=5)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
437
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
438 ### plot for second m/z
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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439 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
440 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,6,3))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
441 abline(v=maxmass2, col="red", lty=5)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
442 title("Control of fold change plot", outer=TRUE)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
443
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
444 ### filter spectra for max m/z to have two vectors, which can be divided
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
445 ### plot spatial distribution of fold change
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
446 ### only possible when there are intensities > 0 in both given m/z ranges
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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447
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
448 if (length(maxmass1)>0&length(maxmass2)>0){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
449 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
450 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
451 foldchange= log2(mass1vector/mass2vector)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
452 fcmatrix = cbind(foldchange, coord(msidata)[,1:2])
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
453
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
454 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange), colour=colo)+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
455 geom_tile() + coord_fixed()+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
456 ggtitle("$label")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
457 theme_bw()+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
458 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
459 theme(text=element_text(family="ArialMT", face="bold", size=12))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
460 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
9
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diff changeset
461 ,space = "Lab", na.value = "black", name ="FC"))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
462 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
463 plot(0,type='n',axes=FALSE,ann=FALSE)
13
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diff changeset
464 title(main=paste("At least one m/z range did not contain any intensity > 0,\n therefore no foldchange plot could be drawn"))}
9
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diff changeset
465
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
466 #end for
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
467 #end if
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
468
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
469 #################### 4) m/z heatmaps #######################################
2
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diff changeset
470
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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diff changeset
471 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
472 if (length(inputcalibrants[,1]) != 0){
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
473 for (mass in 1:length(inputcalibrants[,1])){
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
474
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
475
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
476 image(msidata, mz=inputcalibrants[,1][mass], plusminus=plusminusvalues[mass],
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
477 main= paste0(inputcalibrants[,2][mass], ": ", round(inputcalibrants[,1][mass], digits = 2)," (±",$plusminus_ppm, " ppm)"),
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
478 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
2
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diff changeset
479 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
480 } else {print("4) The input peptide and calibrant m/z were not provided or outside the m/z range")}
2
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diff changeset
481
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
482 #################### 5) Number of peaks per pixel - image ##################
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
483
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
484 ## here every intensity value > 0 counts as pixel
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
485 peaksperpixel = colSums(spectra(msidata)[]> 0, na.rm=TRUE)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
486 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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parents: 1
diff changeset
487
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
488 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
489 geom_tile() + coord_fixed() +
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
490 ggtitle("Number of peaks per spectrum")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
491 theme_bw() +
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
492 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
493 theme(text=element_text(family="ArialMT", face="bold", size=12))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
494 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
495 ,space = "Lab", na.value = "black", name = "# peaks"))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
496
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
497 ## append list for optional tabular output with spectrum values
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
498 colnames(peakscoordarray)[3] = "Number of Peaks"
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
499 spectrum_list[[list_count]] = peakscoordarray
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
500 list_count = list_count+1
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
501
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
502 ############################### 6) TIC image ###############################
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
503
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
504 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
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diff changeset
505 colo = colorRampPalette(
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
506 c("blue", "cyan", "green", "yellow","red"))
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
507 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
508 geom_tile() + coord_fixed() +
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
509 ggtitle("Total Ion Chromatogram")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
510 theme_bw() +
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
511 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
512 theme(text=element_text(family="ArialMT", face="bold", size=12))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
513 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
514 ,space = "Lab", na.value = "black", name = "TIC"))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
515
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
516 ## append list for optional tabular output with spectrum values
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
517 colnames(TICcoordarray)[3] = "TIC per spectrum"
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
518 spectrum_list[[list_count]] = TICcoordarray
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
519 list_count = list_count+1
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
520
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
521 ############################### 7) Most abundant m/z image #################
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
522
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
523 highestmz = apply(spectra(msidata)[],2,which.max)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
524 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz])
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
525 colnames(highestmz_matrix)[3] = "highestmzinDa"
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
526
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
527 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
528 geom_tile() + coord_fixed() +
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
529 ggtitle("Most abundant m/z in each spectrum")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
530 theme_bw() +
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
531 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
532 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z",
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
533 limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))+
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
534 theme(text=element_text(family="ArialMT", face="bold", size=12)))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
535
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
536 ## append list for optional tabular output with spectrum values
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
537 colnames(highestmz_matrix)[3] = "Most abundant m/z"
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
538 spectrum_list[[list_count]] = highestmz_matrix
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
539
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
540
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
541 ## tabular output of spectra values
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
542
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
543 #if $pixel_output:
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
544 print("pixel list")
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
545 pixel_df = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), spectrum_list)
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
546 write.table(pixel_df, file="$pixel_tabular_output", quote = FALSE, row.names = FALSE, col.names=TRUE, sep = "\t")
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
547 #end if
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
548
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
549 ########################## 8) optional pca image for two components #################
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
550
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
551 #if $do_pca:
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
552
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
553 pca = PCA(msidata, ncomp=2)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
554 par(mfrow = c(2,1))
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
555 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
556 image(pca, col=c("black", "white"), strip=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
557
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
558 #end if
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
559
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
560 ################## III) properties over spectra index ######################
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
561 ############################################################################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
562 print("properties over pixels")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
563 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
564
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
565 ########################## 9) number of peaks per spectrum #################
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
566 ## 9a) scatterplot
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
567
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
568 ## order pixels according to annotation groups if annotations are provided
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
569 if (!is.null(levels(msidata\$annotation))){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
570
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
571 pixel_peaks_df = cbind(pixel_name_df, peaksperpixel)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
572 pixel_ordered = pixel_peaks_df[order(pixel_peaks_df\$pixel_name),] ## order pixels according to annotation group names
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
573 pixel_ordered\$annotation_order = 1:ncol(msidata)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
574 plot_colorByDensity(pixel_ordered\$annotation_order, pixel_ordered\$peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
575 title(xlab="Spectra index ordered for annotation groups", line=3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
576 title(ylab="Number of peaks", line=4)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
577 abline(v=abline_vector, lty = 3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
578 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
579 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
580 title(xlab="Spectra index", line=3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
581 title(ylab="Number of peaks", line=4)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
582 }
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
583
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
584 ## 9b) histogram
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
585
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
586 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
587 title(main="Number of peaks per spectrum", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
588 title(ylab="Frequency = # spectra", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
589 abline(v=median(peaksperpixel), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
590
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
591 ## 9c) additional histogram to show contribution of annotation groups
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
592 ## only when pixel annotations were loaded
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
593 if (!is.null(levels(msidata\$annotation))){
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
594
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
595 df_9 = data.frame(peaksperpixel, msidata\$annotation)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
596 colnames(df_9) = c("Npeaks", "annotation")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
597
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
598 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=annotation)) +
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
599 geom_histogram()+ theme_bw()+
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
600 theme(text=element_text(family="ArialMT", face="bold", size=12))+
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
601 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
602 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
603 theme(legend.position="bottom",legend.direction="vertical")+
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
604 labs(title="Number of peaks per spectrum and annotation group", x="Number of peaks per spectrum", y = "Frequency = # spectra") +
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
605 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
606 geom_vline(xintercept = median(peaksperpixel), size = 1, colour = "black",linetype = "dashed")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
607 print(hist_9)}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
608
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
609 ########################## 10) TIC per spectrum ###########################
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
610
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
611 ## 10a)density scatterplot
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
612 par(mfrow = c(2,1), mar=c(5,6,4,2))
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
613
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
614 ## order pixels according to annotation groups if annotations are provided
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
615 if (!is.null(levels(msidata\$annotation))){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
616
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
617 pixel_TIC_df = cbind(pixel_name_df, TICs)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
618 pixel_ordered = pixel_TIC_df[order(pixel_TIC_df\$pixel_name),] ## order pixels according to annotation group names
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
619 pixel_ordered\$annotation_order = 1:ncol(msidata)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
620
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
621 plot_colorByDensity(pixel_ordered\$annotation_order, pixel_ordered\$TICs, ylab = "", xlab = "", main="TIC per spectrum")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
622 title(xlab="Spectra index ordered for annotation groups", line=3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
623 title(ylab="Total ion chromatogram intensity", line=4)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
624 abline(v=abline_vector, lty = 3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
625 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
626 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
627 title(xlab="Spectra index", line=3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
628 title(ylab = "Total ion chromatogram intensity", line=4)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
629 }
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
630
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
631 ## 10b) histogram
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
632 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
633 title(main= "TIC per spectrum", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
634 title(ylab="Frequency = # spectra", line=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
635 abline(v=median(log(TICs[TICs>0])), col="blue")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
636
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
637 ## 10c) additional histogram to show annotation contributions
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
638 ## only when pixel annotations were loaded
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
639 if (!is.null(levels(msidata\$annotation))){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
640 df_10 = data.frame(log(TICs), msidata\$annotation)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
641 colnames(df_10) = c("TICs", "annotation")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
642
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
643 hist_10 = ggplot(df_10, aes(x=TICs, fill=annotation)) +
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
644 geom_histogram()+ theme_bw()+
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
645 theme(text=element_text(family="ArialMT", face="bold", size=12))+
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
646 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
647 theme(legend.position="bottom",legend.direction="vertical")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
648 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
649 labs(title="TIC per spectrum and annotation group", x="log(TIC per spectrum)", y = "Frequency = # spectra") +
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
650 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
651 geom_vline(xintercept = median(log(TICs[TICs>0])), size = 1, colour = "black",linetype = "dashed")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
652 print(hist_10)}
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
653
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
654 ################################## IV) properties over m/z ####################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
655 ############################################################################
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
656 print("properties over m/z")
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
657
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
658 ########################## 11) Histogram of m/z values #####################
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
659
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
660 par(mfrow = c(1, 1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
661 hist(mz(msidata), xlab = "m/z", main="Histogram of m/z values")
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
662
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
663 ########################## 12) Number of peaks per m/z #####################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
664
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
665 peakspermz = rowSums(spectra(msidata)[] > 0 )
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
666
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
667 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
668 ## 12a) scatterplot
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
669 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per m/z", ylab ="")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
670 title(xlab="m/z", line=2.5)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
671 title(ylab = "Number of peaks", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
672 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
673 mtext("Coverage of spectra [%]", 4, line=3, adj=1)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
674
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
675 ## 12b) histogram
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
676 hist(peakspermz, main="", las=1, ylab="", xlab="")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
677 title(ylab = "Frequency", line=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
678 title(main="Number of peaks per m/z", xlab = "Number of peaks per m/z", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
679 abline(v=median(peakspermz), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
680
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
681 ########################## 13) Sum of intensities per m/z ##################
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
682
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
683 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
684 mzTIC = rowSums(spectra(msidata)[]) ## calculate intensity sum for each m/z
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
685
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
686 par(mfrow = c(2,1), mar=c(5,6,4,2))
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
687 ## 13a) scatterplot
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
688 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per m/z", ylab ="")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
689 title(xlab="m/z", line=2.5)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
690 title(ylab="Intensity sum", line=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
691
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
692 ## 13b) histogram
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
693 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
694 title(main="Sum of intensities per m/z", line=2, ylab="")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
695 title(xlab = "log (sum of intensities per m/z)")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
696 title(ylab = "Frequency", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
697 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
698
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
699 ################################## V) intensity plots ########################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
700 ############################################################################
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
701 print("intensity plots")
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
702 ########################## 14) Intensity distribution ######################
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
703
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
704 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
705
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
706 ## 14a) Median intensity over spectra
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
707 medianint_spectra = apply(spectra(msidata), 2, median)
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
708
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
709 ## order pixels according to annotation groups if annotations are provided
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
710 if (!is.null(levels(msidata\$annotation))){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
711
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
712 pixel_median_df = cbind(pixel_name_df, medianint_spectra)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
713 pixel_ordered = pixel_median_df[order(pixel_median_df\$pixel_name),] ## order pixels according to annotation group names
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
714 plot(pixel_ordered\$medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index ordered for annotation groups", ylab="")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
715 title(ylab="Median spectrum intensity", line=4)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
716 abline(v=abline_vector, lty = 3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
717 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
718 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
719 title(ylab="Median spectrum intensity", line=4)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
720 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
721
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
722 ## 14b) histogram:
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
723 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
724 title(main="Log2-transformed intensities", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
725 title(xlab="log2 intensities")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
726 title(ylab="Frequency", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
727 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)])), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
728
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
729 ## 14c) histogram to show contribution of annotation groups
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
730 ## only when annotation tabular was provided
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
731 if (!is.null(levels(msidata\$annotation))){
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
732
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
733 df_13 = data.frame(matrix(,ncol=2, nrow=0))
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
734 for (subsample in levels(msidata\$annotation)){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
735 log2_int_subsample = log2(spectra(msidata)[,msidata\$annotation==subsample])
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
736 df_subsample = data.frame(as.numeric(log2_int_subsample))
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
737 df_subsample\$annotation = subsample
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
738 df_13 = rbind(df_13, df_subsample)}
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
739 df_13\$annotation = as.factor(df_13\$annotation)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
740 colnames(df_13) = c("logint", "annotation")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
741
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
742 hist_13 = ggplot(df_13, aes(x=logint, fill=annotation)) +
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
743 geom_histogram()+ theme_bw()+
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
744 theme(text=element_text(family="ArialMT", face="bold", size=12))+
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
745 labs(title="Log2-transformed intensities per sample", x="log2 intensities", y = "Frequency") +
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
746 theme(plot.title = element_text(hjust = 0.5))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
747 theme(legend.position="bottom",legend.direction="vertical")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
748 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
749 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
750 geom_vline(xintercept = median(log2(spectra(msidata)[(spectra(msidata)>0)])), size = 1, colour = "black",linetype = "dashed")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
751 print(hist_13)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
752
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
753 ## 14d) boxplots to visualize in a different way the intensity distributions
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
754 par(mfrow = c(1,1), cex.axis=1.3, cex.lab=1.3, mar=c(13.1,4.1,5.1,2.1))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
755
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
756 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata))
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
757 for (subsample in levels(msidata\$annotation)){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
758 mean_mz_sample = rowMeans(spectra(msidata)[,msidata\$annotation==subsample])
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
759 mean_matrix = cbind(mean_matrix, mean_mz_sample)}
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
760
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
761 boxplot(log2(mean_matrix), ylab = "log2 mean intensity per m/z", main="Mean intensities per m/z and annotation group", xaxt = "n")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
762 (axis(1, at = c(1:number_combined), labels=levels(msidata\$annotation), cex.axis=cex_boxplot, las=2))
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
763 }
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
764
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
765 ################################## VI) Mass spectra and m/z accuracy ########################
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
766 ############################################################################
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
767 print("Mass spectra and m/z accuracy")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
768
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
769 ############################ 15) Mass spectra ##############################
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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diff changeset
770
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
771 par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
772 pixels_for_plot = c(round(length(pixelnumber)/2, , digits=0), round(length(pixelnumber)/4, , digits=0), round(length(pixelnumber)/4*3, , digits=0))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
773 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
774 plot(msidata, pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2])))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
775 plot(msidata, pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2])))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
776 plot(msidata, pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2])))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
777
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
778 ################### 16) Zoomed in mass spectra for calibrants ##############
2
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galaxyp
parents: 1
diff changeset
779
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
780 count = 1
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
781 differencevector = numeric()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
782 differencevector2 = vector()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
783
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
784 if (length(inputcalibrantmasses) != 0){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
785
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
786 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
787 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses)) * inputcalibrantmasses
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
788
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
789 for (mass in 1:length(inputcalibrantmasses)){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
790
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
791 ### define the plot window with xmin und xmax
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
792 minmasspixel = features(msidata, mz=inputcalibrantmasses[mass]-1)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
793 maxmasspixel = features(msidata, mz=inputcalibrantmasses[mass]+3)
0
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parents:
diff changeset
794
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
795 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
796 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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diff changeset
797
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
798 if (nrow(filtered_data) > 0 & sum(spectra(filtered_data)) > 0){
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
799 maxmassrow = rowMeans(spectra(filtered_data)) ## for each m/z average intensity is calculated
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
800 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highest average intensity in m/z range
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
801 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
802 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
803 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
804 ppmdifference = NA
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
805 maxvalue = NA}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
806 differencevector[mass] = round(ppmdifference, digits=2)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
807
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
808 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
809 mznumber = features(msidata, mz = inputcalibrantmasses[mass]) ### gives featurenumber which is closest to given m/z
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
810 mzvalue = mz(msidata)[mznumber] ### gives closest m/z
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
811 mzdifference2 = mzvalue - inputcalibrantmasses[mass]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
812 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
813 differencevector2[mass] = round(ppmdifference2, digits=2)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
814
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
815 par(mfrow = c(2, 2), oma=c(0,0,2,0))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
816 plot(msidata[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "average spectrum")
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
817 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
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446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
818 abline(v=c(maxvalue), col="red", lty=2)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
819 abline(v=c(mzvalue), col="green2", lty=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
820 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2])))
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
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diff changeset
821 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
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446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
822 abline(v=c(maxvalue), col="red", lty=2)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
823 abline(v=c(mzvalue), col="green2", lty=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
824 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2])))
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
825 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
826 abline(v=c(maxvalue), col="red", lty=2)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
827 abline(v=c(mzvalue), col="green2", lty=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
828 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2])))
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
829 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
830 abline(v=c(maxvalue), col="red", lty=2)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
831 abline(v=c(mzvalue), col="green2", lty=4)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
832 title(paste0("theor. m/z: ", inputcalibrants[count,1]), col.main="blue", outer=TRUE, line=0, adj=0.074)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
833 title(paste0("most abundant m/z: ", round(maxvalue, digits=4)), col.main="red", outer=TRUE, line=0, adj=0.49)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
834 title(paste0("closest m/z: ", round(mzvalue, digits=4)), col.main="green2", outer=TRUE, line=0, adj=0.93)
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
835
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
836 ### 16b) one large extra plot with different colours for different pixel annotation groups
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
837
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
838 if (!is.null(levels(msidata\$annotation))){
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
839 if (number_combined < 10){
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
840 key_zoomed = TRUE
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
841 }else{key_zoomed = FALSE}
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
842 par(mfrow = c(1, 1))
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
843 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),main="Average spectrum per annotation group",
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
844 pixel.groups=msidata\$annotation, key=key_zoomed, col=hue_pal()(number_combined),superpose=TRUE)
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
845 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="black", lty=c(3,1,3))
12
d8e584de1e34 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a0cadd9fe40da0094dc87bbf5e06a323973a0b42
galaxyp
parents: 11
diff changeset
846 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
847 count=count+1
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
848 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
849
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
850 ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range#########
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
851
15
898dec99d9fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 14
diff changeset
852 par(mfrow = c(1,1))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
853 ### plot the ppm difference calculated above: theor. m/z value to highest m/z value:
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
854
7
ae9d7703ff27 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 6
diff changeset
855 calibrant_names = as.character(inputcalibrants[,2])
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
856 diff_df = data.frame(differencevector, calibrant_names)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
857
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
858 if (sum(is.na(diff_df[,1])) == nrow(diff_df)){
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
859 plot(0,type='n',axes=FALSE,ann=FALSE)
15
898dec99d9fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 14
diff changeset
860 title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range"))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
861 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
862
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
863 diff_plot1=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
864 labs(title="Average m/z error (max. average intensity vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
15
898dec99d9fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 14
diff changeset
865 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
866 geom_text(aes(label=differencevector), vjust=-0.3, size=5.5, col="blue") +
15
898dec99d9fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 14
diff changeset
867 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
868
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
869 print(diff_plot1)
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
870 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
871
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
872 ######### 18) ppm difference input calibrant m/z and closest m/z ###########
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
873
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
874 ### plot the ppm difference calculated above theor. m/z value to closest m/z value:
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
875
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
876 differencevector2 = round(differencevector2, digits=2)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
877 calibrant_names = as.character(inputcalibrants[,2])
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
878 diff_df = data.frame(differencevector2, calibrant_names)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
879
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
880 diff_plot2=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
881 labs(title="Average m/z error (closest measured m/z vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
15
898dec99d9fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 14
diff changeset
882 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
883 geom_text(aes(label=differencevector2), vjust=-0.3, size=5.5, col="blue")+
15
898dec99d9fc planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 620a469e20836b921b6c0147421c8a4268b66ebd
galaxyp
parents: 14
diff changeset
884 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
885
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
886 print(diff_plot2)
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
887
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
888 #################### 19) ppm difference over pixels #####################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
889
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
890 par(mfrow = c(1,1))
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
891 mycolours = c("darkgrey", "darkblue", "blue", "green" , "red", "orange", "yellow", "magenta", "olivedrab1", "lightseagreen")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
892 count = 1
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
893 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata)))
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
894 for (calibrant in inputcalibrantmasses){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
895 ### find m/z with the highest mean intensity in m/z range, if no m/z in the range, ppm differences for this calibrant will be NA
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
896 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],]
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
897
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
898 if (nrow(filtered_data) > 0){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
899 ### filtered for m/z range, find max peak in each spectrum (pixel)(
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
900 ppm_vector = numeric()
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
901 for (pixel_count in 1:ncol(filtered_data)){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
902 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])]
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
903
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
904 mzdiff = mz_max - calibrant
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
905 ppmdiff = mzdiff/calibrant*1000000
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
906
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
907 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
908 if (max(spectra(filtered_data)[,pixel_count]) == 0){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
909 ppmdiff = NA}
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
910 ppm_vector[pixel_count] = ppmdiff}
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
911
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
912 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
913 ppm_vector = rep(NA, ncol(msidata))
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
914 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
915
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
916 ppm_df = cbind(ppm_df, ppm_vector)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
917 count=count+1
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
918 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
919
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
920 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_df)){
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
921 plot(0,type='n',axes=FALSE,ann=FALSE)
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
922 title(main=paste("plot 19: no peaks in the chosen region, repeat with higher ppm range"))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
923 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
924
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
925 ### plot ppm differences over pixels (spectra index)
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
926 par(mar=c(4.1, 4.1, 4.1, 7.5))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
927
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
928 ## if annotations are provided, pixel index is ordered according to annotation groups
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
929 if (!is.null(levels(msidata\$annotation))){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
930 ppm_df_pixels =cbind(pixel_name_df, ppm_df)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
931 pixel_ordered = ppm_df_pixels[order(ppm_df_pixels\$pixel_name),] ## order pixels according to annotation group names
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
932
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
933 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index ordered for annotation groups", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
934
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
935 for (each_cal in 1:ncol(ppm_df)){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
936 lines(pixel_ordered[,each_cal+2], col=mycolours[each_cal], type="p")}
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
937 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
938 abline(v=abline_vector, lty = 3)
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
939 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
940
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
941 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)")
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
942
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
943 for (each_cal in 1:ncol(ppm_df)){
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
944 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
945 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)}
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
946 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
947
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
948 }else{print("plot 16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")}
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
949 }else{
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
950 print("inputfile has no intensities > 0")
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
951 }
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
952 dev.off()
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
953
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
954
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
955 ]]></configfile>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
956 </configfiles>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
957 <inputs>
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
958 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
959 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
960 <conditional name="processed_cond">
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
961 <param name="processed_file" type="select" label="Is the input file a processed imzML file ">
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
962 <option value="no_processed" selected="True">not a processed imzML</option>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
963 <option value="processed">processed imzML</option>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
964 </param>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
965 <when value="no_processed"/>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
966 <when value="processed">
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
967 <param name="accuracy" type="float" value="50" label="Mass accuracy to which the m/z values will be binned" help="This should be set to the native accuracy of the mass spectrometer, if known"/>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
968 <param name="units" display="radio" type="select" label="Unit of the mass accuracy" help="either m/z or ppm">
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
969 <option value="mz" >mz</option>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
970 <option value="ppm" selected="True" >ppm</option>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
971 </param>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
972 </when>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
973 </conditional>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
974 <conditional name="tabular_annotation">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
975 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for QC plots">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
976 <option value="no_annotation" selected="True">pixels belong into one group only</option>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
977 <option value="yes_annotation">use pixel annotation from a tabular file</option>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
978 </param>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
979 <when value="yes_annotation">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
980 <param name="annotation_file" type="data" format="tabular" label="Use annotations from tabular file"
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
981 help="Tabular file with three columns: x values, y values and pixel annotations"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
982 <param name="column_x" data_ref="annotation_file" label="Column with x values" type="data_column"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
983 <param name="column_y" data_ref="annotation_file" label="Column with y values" type="data_column"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
984 <param name="column_names" data_ref="annotation_file" label="Column with pixel annotations" type="data_column"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
985 </when>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
986 <when value="no_annotation"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
987 </conditional>
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
988 <param name="filename" type="text" value="" optional="true" label="Title" help="will appear as header in the quality report, if nothing given input dataset name is used"/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
989 <param name="calibrant_file" type="data" optional="true" format="tabular"
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
990 label="File with internal calibrants" help="first column: m/z, second column: name (optional), tabular file"/>
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
991 <param name="plusminus_ppm" value="50" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z"/>
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
992 <param name="do_pca" type="boolean" display="radio" label="PCA with 2 components"/>
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
993 <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10">
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
994 <param name="mass1" value="1111" type="float" label="M/z 1" help="First m/z"/>
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
995 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/>
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
996 <param name="distance" value="0.25" type="float" label="M/z range" help="Plusminus m/z window added to input m/z. In both m/z ranges the maximum intensity is used to calculate the fold change"/>
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
997 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
998 </repeat>
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
999 <param name="pixel_output" type="boolean" display="radio" label="Tabular output with spectra information"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1000 </inputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1001 <outputs>
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1002 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "$infile.display_name QC_report"/>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1003 <data format="tabular" name="pixel_tabular_output" label="$infile.display_name spectra information">
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1004 <filter>pixel_output</filter>
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1005 </data>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1006 </outputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1007 <tests>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1008 <test expect_num_outputs="2">
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1009 <param name="infile" value="" ftype="imzml">
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1010 <composite_data value="Example_Processed.imzML"/>
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1011 <composite_data value="Example_Processed.ibd"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1012 </param>
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1013 <conditional name="processed_cond">
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1014 <param name="processed_file" value="processed"/>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1015 <param name="accuracy" value="200"/>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1016 <param name="units" value="ppm"/>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1017 </conditional>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1018 <conditional name="tabular_annotation">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1019 <param name="load_annotation" value="no_annotation"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1020 </conditional>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1021 <param name="calibrant_file" value="inputcalibrantfile1.txt"/>
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1022 <param name="plusminus_ppm" value="100"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1023 <param name="filename" value="Testfile_imzml"/>
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1024 <param name="do_pca" value="True"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1025 <repeat name="calibrantratio">
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1026 <param name="mass1" value="328.9"/>
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1027 <param name="mass2" value="398.8"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1028 <param name="distance" value="0.25"/>
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1029 <param name="filenameratioplot" value = "Ratio of mass1 (328.9) / mass2 (398.8)"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1030 </repeat>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1031 <param name="pixel_output" value="True"/>
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1032 <output name="pixel_tabular_output" file="spectra_info_imzml.txt"/>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1033 <output name="plots" file="QC_imzml.pdf" compare="sim_size" delta="20000"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1034 </test>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1035
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1036 <test expect_num_outputs="1">
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1037 <param name="infile" value="" ftype="analyze75">
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1038 <composite_data value="Analyze75.hdr"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1039 <composite_data value="Analyze75.img"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1040 <composite_data value="Analyze75.t2m"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1041 </param>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1042 <conditional name="tabular_annotation">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1043 <param name="load_annotation" value="no_annotation"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1044 </conditional>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1045 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1046 <param name="filename" value="Testfile_analyze75"/>
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1047 <param name="do_pca" value="True"/>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1048 <output name="plots" file="QC_analyze75.pdf" compare="sim_size" delta="20000"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1049 </test>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1050
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1051 <test expect_num_outputs="2">
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1052 <param name="infile" value="123_combined.RData" ftype="rdata"/>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1053
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1054 <conditional name="tabular_annotation">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1055 <param name="load_annotation" value="yes_annotation"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1056 <param name="annotation_file" value="annotations_rdata.tabular"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1057 <param name="column_x" value="1"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1058 <param name="column_y" value="2"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1059 <param name="column_names" value="3"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1060 </conditional>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1061 <param name="calibrant_file" value="inputcalibrantfile1.txt"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1062 <param name="plusminus_ppm" value="100"/>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1063 <param name="filename" value="Testfile_rdata"/>
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1064 <param name="do_pca" value="True"/>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1065 <param name="pixel_output" value="True"/>
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1066 <output name="pixel_tabular_output" file="spectra_info_123_combi.txt"/>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1067 <output name="plots" file="QC_rdata.pdf" compare="sim_size" delta="20000"/>
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1068 </test>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1069 <test expect_num_outputs="1">
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1070 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1071 <conditional name="tabular_annotation">
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1072 <param name="load_annotation" value="no_annotation"/>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1073 </conditional>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1074 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1075 <param name="filename" value="Testfile_rdata"/>
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
1076 <param name="do_pca" value="False"/>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1077 <output name="plots" file="QC_empty_spectra.pdf" compare="sim_size" delta="20000"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1078 </test>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1079 </tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1080 <help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1081 <![CDATA[
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1082 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1083
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1084 This tool uses Cardinal to read files and create a quality control report with descriptive plots for mass spectrometry imaging data.
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1085
16
f56166082222 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 15
diff changeset
1086 Input data: 3 types of MSI data can be used:
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1087
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1088 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1089 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1090 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
16
f56166082222 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 15
diff changeset
1091 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts.
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1092 - optional: tabular file with pixel annotations: x and y values in separate columns and the corresponding annotation in a third column
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1093
16
f56166082222 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5feaf3d0e0da8cef1241fecc1f4d6f81324594e6
galaxyp
parents: 15
diff changeset
1094
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1095 Options:
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
1096
9
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galaxyp
parents: 8
diff changeset
1097 - internal calibrants are used for m/z heatmaps (x-y grid), heatmap of number of calibrants per spectrum (x-y grid), zoomed in mass spectra, m/z accuracy
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1098 - optional fold change plot: draws a heatmap (x-y grid) for the fold change of two m/z (log2(intensity ratio))
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1099
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1100 Output:
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 7
diff changeset
1101
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1102 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1103 - optional spectra information as tabular file with annotation (if provided), numbers of calibrants (needs valid calibrants), numbers of peaks, TIC and most abundant m/z in each spectrum
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1104
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1105 Tip:
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
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parents: 7
diff changeset
1106
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1107 - For additional m/z heatmaps use the MSI ion images tool and to plot more mass spectra use the MSI mass spectra tool.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1108
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1109 ----------------------------------------------------------------------------------------------------------------------------------------------------
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1110
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1111 Overview of the QC report plots:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
1112
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
1113 - (annot): this plots will only be drawn if pixel annotations are loaded via a tabular file
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1114 - (cal): this plots will only be drawn if a tabular file with at least one valid calibrant m/z is provided
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1115 - (FC): this plots will only be drawn if the optional fold change image is selected
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1116 - Vertical lines in histograms represent median values. In density scatter plots the colour changes from blue to green, yellow and red the more points are overlayed.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1117
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
1118 - Overview of file properties: Numbers and ranges for m/z features and pixels are given. Median and range across all intensity values are provided. Intensities > 0 gives the percentage of m/z-pixel pairs with an intensity above zero. The number of empty spectra (TIC = 0), the median number of peaks (intensities > 0) per spectra as well as the median TIC (total ion chromatogram) are given. The processing status of the file is provided as well as the number of valid calibrants from the provided tabular file.> 0 (Intensities > 0).
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1119
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1120 x-y images (pixel/spectra information):
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
1121
14
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diff changeset
1122 - (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour.
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
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diff changeset
1123 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order. If annotation file is provided pixels are ordered according to annotation groups.
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
1124 - (cal) Number of calibrants per pixel: In every spectrum the calibrant m/z window (calibrant m/z plusminus 'ppm range') is searched for peaks (intensity > 0). Calibrants are considered present in a spectrum when they have at least one peak in their m/z window.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1125 - (FC) Control of fold change plot: For both input m/z a zoomed in average spectrum is drawn with the input m/z as blue dashed line, the m/z range as blue dotted lines and the maximum intensity in the m/z window with a red line.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1126 - (FC) Fold change image: For each spectrum the intensities of the two optimal m/z features (red lines in control plots) are divided and log2 transformed to obtain the fold change, which is then plotted as a heatmap.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1127 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z. The intensities are averaged within the calibrant m/z window (ppm range).
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1128 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1129 - Total ion chromatogram: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1130 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1131 - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1132
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1133 Properties over spectra/pixels:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
1134
14
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galaxyp
parents: 13
diff changeset
1135 - Number of peaks per spectrum: Scatter plot and histogram showing the number of intensities > 0 for each spectrum. If annotation tabular file is provided, the pixels are sorted according to annotation groups and the dotted lines in the scatter plot separate spectra of different annotation groups.
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1136 - (annot) Number of peaks per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1137 - TIC per spectrum: Scatter plot and histogram showing the sum of all intensities per spectrum (TIC). Dotted lines in the scatter plot separate spectra of different annotation groups.
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
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diff changeset
1138 - (annot) TIC per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1139
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1140 Properties over m/z features:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1141
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1142 - Histogram of m/z values: Histogram of all m/z values (complete m/z axis)
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1143 - Number of peaks per m/z: Scatter plot and histogram giving the number of intensities > 0 for each m/z.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1144 - Sum of intensities per m/z: Scatter plot and histogram of the sum of all intensities per m/z.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1145
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1146 Intensity plots:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1147
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1148 - Median intensity per spectrum: Scatter plot in which each point represents the median intensity for one spectrum. Dotted lines in the scatter plot separate spectra of different annotation groups.
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1149 - Log2-transformed intensities: Histogram of log2-transformed intensities.
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1150 - (annot) log2-transformed intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group.
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1151 - (annot) Mean intensities per m/z and annotation group: For all pixels of an annotation group the mean intensity for each m/z is calculated and shown as boxplot.
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1152
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1153 Mass spectra and m/z accuracy:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1154
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1155 - Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from single pixels (spectra).
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1156 - (cal) For each calibrant four zoomed in mass spectrum are drawn: The first shows the average intensities over all spectra and the other three are single mass spectra. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window.
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1157 - (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately.
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1158 - (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1159 - (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra.
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1160 - (cal) Difference m/z with max. average intensity vs. theor. m/z (per spectrum): For each spectrum the ppm difference between the m/z with the highest average intensity and the theoretical m/z are plotted. The calibrants have different plotting colours. Dashed lines separate spectra of different annotation groups.
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1161
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1162
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1163 ]]>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1164 </help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
1165 <citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1166 <citation type="doi">10.1093/bioinformatics/btv146</citation>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1167 </citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
1168 </tool>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
1169