Mercurial > repos > galaxyp > msi_qualitycontrol

annotate msi_qualitycontrol.xml @ 14:5aad8ef93356 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
author galaxyp
date Tue, 24 Jul 2018 04:51:59 -0400
parents 0a6923b31ed0
children 898dec99d9fc
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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.5">
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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>
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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>
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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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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 $infile.ext == 'analyze75'
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49 msidata = readAnalyze('infile')
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50 #else
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51 load('infile.RData')
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52 #end if
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53
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54 ## create full matrix to make processed imzML files compatible with segmentation and other steps
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55 iData(msidata) <- iData(msidata)[]
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57 ## remove duplicated coordinates
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58 print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))
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59 msidata <- msidata[,!duplicated(coord(msidata))]
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60
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61 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
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62
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63 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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64
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65 ## read and extract x,y,annotation information
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66 input_tabular = read.delim("$tabular_annotation.annotation_file", header = TRUE, stringsAsFactors = FALSE)
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67 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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68 annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
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69 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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71 ## merge with coordinate information of msidata
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72 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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73 colnames(msidata_coordinates)[3] = "pixel_index"
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74 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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75 merged_annotation[is.na(merged_annotation)] = "NA"
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76 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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77 msidata\$annotation = as.factor(merged_annotation[,4])
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78
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79 #end if
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80
0
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81 ###################################### file properties in numbers ######################
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82
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83 ## Number of features (m/z)
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84 maxfeatures = length(features(msidata))
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85 ## Range m/z
0
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86 minmz = round(min(mz(msidata)), digits=2)
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87 maxmz = round(max(mz(msidata)), digits=2)
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88 ## Number of spectra (pixels)
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89 pixelcount = length(pixels(msidata))
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90 ## Range x coordinates
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91 minimumx = min(coord(msidata)[,1])
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92 maximumx = max(coord(msidata)[,1])
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93 ## Range y coordinates
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94 minimumy = min(coord(msidata)[,2])
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95 maximumy = max(coord(msidata)[,2])
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96 ## Range of intensities
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97 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
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98 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
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99 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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100 ## Number of intensities > 0
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101 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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102 ## Spectra multiplied with m/z (potential number of peaks)
0
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103 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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104 ## Percentage of intensities > 0
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105 percpeaks = round(npeaks/numpeaks*100, digits=2)
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106 ## Number of empty TICs
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107 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
0
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108 NumemptyTIC = sum(TICs == 0)
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109 ## Median TIC
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110 medTIC = round(median(TICs), digits=2)
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111 ## Median peaks per spectrum
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112 medpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE)
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113 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))
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114
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115 ## Processing informations
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116 processinginfo = processingData(msidata)
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117 centroidedinfo = processinginfo@centroided
0
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118
9
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119 ## if TRUE write processinginfo if FALSE write FALSE
0
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120
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121 ## normalization
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122 if (length(processinginfo@normalization) == 0) {
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123 normalizationinfo='FALSE'
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124 } else {
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125 normalizationinfo=processinginfo@normalization
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126 }
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127 ## smoothing
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128 if (length(processinginfo@smoothing) == 0) {
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129 smoothinginfo='FALSE'
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130 } else {
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131 smoothinginfo=processinginfo@smoothing
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132 }
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133 ## baseline
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134 if (length(processinginfo@baselineReduction) == 0) {
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135 baselinereductioninfo='FALSE'
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136 } else {
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137 baselinereductioninfo=processinginfo@baselineReduction
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138 }
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139 ## peak picking
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140 if (length(processinginfo@peakPicking) == 0) {
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141 peakpickinginfo='FALSE'
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142 } else {
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143 peakpickinginfo=processinginfo@peakPicking
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144 }
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145
9
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146 ############## Read and filter tabular file with m/z ###########################
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147
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148 ### reading calibrant file:
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149
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150 #if $calibrant_file:
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151
4
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152 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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153 if (ncol(calibrant_list) == 1)
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154 {calibrant_list = cbind(calibrant_list, calibrant_list)} ## if there is just one column dublicate it to have a names column
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155
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156 ### calculate how many input calibrant m/z are valid:
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157
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158 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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159 number_calibrants_in = length(calibrant_list[,1])
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160 number_calibrants_valid = length(inputcalibrants[,1])
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161
4
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162 #else
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163
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164 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
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165 number_calibrants_in = 0
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166 number_calibrants_valid = 0
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167
4
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168 #end if
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169
11
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170 ## rename input dataframe and extract m/z
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171 colnames(inputcalibrants) = c("m/z", "name")
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172 inputcalibrantmasses = inputcalibrants[,1]
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173
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174
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175 ######################################## PDF #############################################
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176 ##########################################################################################
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177 ##########################################################################################
0
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178
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179 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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180 plot(0,type='n',axes=FALSE,ann=FALSE)
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181
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182 ## if no filename is given, name of file in Galaxy history is used
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183
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184 #if not $filename:
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185 #set $filename = $infile.display_name
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186 #end if
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187
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188 title(main=paste("$filename"))
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189
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190 ################# I) file properties in numbers ################################
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191 ################################################################################
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192 print("properties in numbers")
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193
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194 properties = c("Number of m/z features",
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195 "Range of m/z values",
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196 "Number of pixels",
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197 "Range of x coordinates",
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198 "Range of y coordinates",
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199 "Range of intensities",
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200 "Median of intensities",
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201 "Intensities > 0",
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202 "Number of empty spectra",
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203 "Median TIC",
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204 "Median # peaks per spectrum",
0
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205 "Normalization",
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206 "Smoothing",
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207 "Baseline reduction",
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208 "Peak picking",
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209 "Centroided",
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210 paste0("calibrants (#valid/#input) in \n", "$calibrant_file.display_name"))
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211
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212 values = c(paste0(maxfeatures),
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213 paste0(minmz, " - ", maxmz),
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214 paste0(pixelcount),
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215 paste0(minimumx, " - ", maximumx),
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216 paste0(minimumy, " - ", maximumy),
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217 paste0(minint, " - ", maxint),
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218 paste0(medint),
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219 paste0(percpeaks, " %"),
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220 paste0(NumemptyTIC),
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221 paste0(medTIC),
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222 paste0(medpeaks),
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223 paste0(normalizationinfo),
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224 paste0(smoothinginfo),
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225 paste0(baselinereductioninfo),
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226 paste0(peakpickinginfo),
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227 paste0(centroidedinfo),
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228 paste0(number_calibrants_valid, " / ", number_calibrants_in))
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229
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230 property_df = data.frame(properties, values)
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231
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232 grid.table(property_df, rows= NULL)
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233
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234 ####################### II) x-y images #######################################
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235 ##############################################################################
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236 print("x-y images")
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237
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238 ## only do plots for file with intensity peaks
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239 if (npeaks > 0){
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240 ## function for density plots
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241 plot_colorByDensity = function(x1,x2,
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242 ylim=c(min(x2),max(x2)),
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243 xlim=c(min(x1),max(x1)),
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244 xlab="",ylab="",main=""){
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245 df = data.frame(x1,x2)
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246 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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247 df\$dens = col2rgb(x)[1,] + 1L
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248 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
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249 df\$col = cols[df\$dens]
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250 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
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251 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
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252
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253 ## start list for optional spectrum values output
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254 spectrum_list = list()
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255 list_count = 1
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256
9
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257 ################### 0) overview for combined data ###########################
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258
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259 ### only for previously combined data, same plot as in combine QC pdf
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260
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261 if (!is.null(levels(msidata\$annotation))){
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262 number_combined = length(levels(msidata\$annotation))
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263
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264 ## the more annotation groups a file has the smaller will be the legend
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265 if (number_combined<20){
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266 legend_size = 10
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267 cex_boxplot = 1
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268 }else if (number_combined>20 && number_combined<40){
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269 legend_size = 9
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270 cex_boxplot = 0.8
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271 }else if (number_combined>40 && number_combined<60){
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272 legend_size = 8
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273 cex_boxplot = 0.6
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274 }else if (number_combined>60 && number_combined<100){
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275 legend_size = 7
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276 cex_boxplot = 0.5
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277 }else{
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278 legend_size = 6
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279 cex_boxplot = 0.3
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280 }
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281
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282 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
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283 colnames(position_df)[3] = annotation_name
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284
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285 ## append list for optional tabular output with spectrum values
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286 spectrum_list[[list_count]] = position_df
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287 list_count = list_count+1
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288
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289 colnames(position_df)[3] = "Annotation"
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290 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=Annotation))+
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291 geom_tile() +
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292 coord_fixed()+
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293 ggtitle("Spatial orientation of combined data")+
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294 theme_bw()+
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295 theme(plot.title = element_text(hjust = 0.5))+
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296 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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297 theme(legend.position="bottom",legend.direction="vertical")+
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298 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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299 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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300
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301 print(combine_plot)
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302
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303 ### order pixels according to annotation - this gives a new pixel/spectra index order according to the annotation groups
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304 pixel_name_df = data.frame(pixels(msidata), msidata\$annotation)
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305 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
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306
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307 pixel_name_df_ordered = pixel_name_df[order(pixel_name_df\$pixel_name),]
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308 pixel_name_df_ordered\$annotated_order = 1:ncol(msidata)
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309 last_pixel = aggregate(annotated_order~pixel_name, data = pixel_name_df_ordered, max)
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310
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311 pixel_vector = last_pixel[,2]
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312 abline_vector = pixel_vector[1:number_combined-1]
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313 print(abline_vector)
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314 }
0
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315
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316 ################### 1) Pixel order image ###################################
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317
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318 pixelnumber = 1:pixelcount
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319 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
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320 gg_title = "Pixel order"
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321
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322 ## order pixels according to annotation groups if annotations are provided
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323 if (!is.null(levels(msidata\$annotation))){
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324 pixelxyarray = pixelxyarray[match(pixel_name_df_ordered\$pixel_number, pixelxyarray\$pixelnumber),]
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325 pixelxyarray\$pixelnumber = 1:ncol(msidata)
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326 gg_title = "Pixel ordered for annotation groups"
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327 }
0
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328
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329 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+
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330 geom_tile() + coord_fixed()+
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331 ggtitle(gg_title) + theme_bw()+
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332 theme(plot.title = element_text(hjust = 0.5))+
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333 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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334 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
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335 space = "Lab", na.value = "black", name = "Pixel\nnumber"))
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336
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337 ################ 2) Number of calibrants per spectrum ######################
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338
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339 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
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340 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
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341
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342 ## plot only possible when there is at least one valid calibrant
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343 if (length(inputcalibrantmasses) != 0){
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344
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345 ## calculate plusminus values in m/z for each calibrant
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346 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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347
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348 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
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349
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350 for (mass in 1:length(inputcalibrantmasses)){
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351
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352 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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353
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354 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){
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355
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356 ## intensity of all m/z > 0
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357 intensity_sum = colSums(spectra(filtered_data)[], na.rm=TRUE) > 0
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358
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359 }else 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 only m/z > 0
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362 intensity_sum = spectra(filtered_data)[] > 0
0
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363
14
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364 }else{
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365
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366 intensity_sum = rep(FALSE, ncol(filtered_data))}
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367
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368 ## for each pixel add sum of intensities > 0 in the given m/z range
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369 pixelmatrix = rbind(pixelmatrix, intensity_sum)
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370 }
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diff changeset
371
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372 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
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373 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
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374 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
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375 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
0
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376
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377 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+
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378 geom_tile() + coord_fixed() +
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379 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) +
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380 theme_bw() +
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381 theme(plot.title = element_text(hjust = 0.5))+
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382 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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383 scale_fill_manual(values = mycolours[1:length(countvector)],
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384 na.value = "black", name = "# calibrants"))
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diff changeset
385
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386 ## append list for optional tabular output with spectrum values
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387 colnames(countdf)[3] = "Number of Calibrants"
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388 spectrum_list[[list_count]] = countdf
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389 list_count = list_count+1
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diff changeset
390
9
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391 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
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392
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393 ########################## 3) fold change image ###########################
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394
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395 #if $calibrantratio:
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396 #for $foldchanges in $calibrantratio:
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397 mass1 = $foldchanges.mass1
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398 mass2 = $foldchanges.mass2
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399 distance = $foldchanges.distance
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400
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401 ### if user did not write a label use input m/z as label
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402 #if not str($foldchanges.filenameratioplot).strip():
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403 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
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diff changeset
404 #else:
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405 #set $label = $foldchanges.filenameratioplot
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diff changeset
406 #end if
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diff changeset
407
9
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diff changeset
408 ### filter msidata for given m/z range (for both input m/z)
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409 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,]
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diff changeset
410 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,]
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411
9
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412 ### find m/z in the two given ranges with the highest mean intensity
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413 ### this two m/z will be used to calculate the fold change (red line in plot)
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diff changeset
414 maxmassrow1 = rowMeans(spectra(filtered_data1), na.rm=TRUE)
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415 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)]
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416 maxmassrow2 = rowMeans(spectra(filtered_data2), na.rm=TRUE)
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417 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)]
2
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418
9
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419 ### plot legend: chosen value in blue, distance in blue, max m/z in red
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420 ### m/z range for each plot (fixed range of 5 Da)
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421 ### xlim does not work because it does not adjust for the max. intensities within the range
2
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diff changeset
422 mzdown1 = features(msidata, mz = mass1-2)
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diff changeset
423 mzup1 = features(msidata, mz = mass1+3)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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424 mzdown2 = features(msidata, mz = mass2-2)
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diff changeset
425 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
diff changeset
426
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
427 ### 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
parents: 1
diff changeset
428 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
galaxyp
parents: 1
diff changeset
429 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
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
430 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
431 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
432
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
433 ### plot for second 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
434 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
435 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
436 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
parents: 1
diff changeset
437 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
438
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
439 ### 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
parents: 8
diff changeset
440 ### 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
parents: 8
diff changeset
441 ### 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
diff changeset
442
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
443 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
parents: 8
diff changeset
444 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
parents: 8
diff changeset
445 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
parents: 8
diff changeset
446 foldchange= log2(mass1vector/mass2vector)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
447 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
parents:
diff changeset
448
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
449 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
galaxyp
parents: 9
diff changeset
450 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
451 ggtitle("$label")+
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
452 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
453 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
454 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
455 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
456 ,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
galaxyp
parents: 8
diff changeset
457 }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
458 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
459 title(main=paste("At least one m/z range did not contain any intensity > 0,\n therefore no foldchange plot could be drawn"))}
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
460
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
461 #end for
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
462 #end if
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
463
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
464 #################### 4) m/z heatmaps #######################################
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
465
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
466 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=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
467 if (length(inputcalibrants[,1]) != 0){
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
468 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
galaxyp
parents: 10
diff changeset
469
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
470
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
471 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
galaxyp
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diff changeset
472 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
galaxyp
parents: 9
diff changeset
473 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
474 }
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
475 } else {print("4) The input peptide and calibrant 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
476
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
477 #################### 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
galaxyp
parents: 1
diff changeset
478
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
479 ## 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
parents: 12
diff changeset
480 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
parents: 5
diff changeset
481 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
galaxyp
parents: 1
diff changeset
482
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
483 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
parents: 9
diff changeset
484 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
485 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
parents: 9
diff changeset
486 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
487 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
488 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
489 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
490 ,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
491
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
492 ## 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
493 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
parents: 9
diff changeset
494 spectrum_list[[list_count]] = peakscoordarray
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
495 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
496
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
497 ############################### 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
498
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
499 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
parents: 3
diff changeset
500 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
501 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
502 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
503 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
504 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
505 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
506 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
507 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
508 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
509 ,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
510
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
511 ## 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
512 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
513 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
514 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
515
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
516 ############################### 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
517
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
518 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
519 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
520 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
521
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
522 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
523 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
524 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
525 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
526 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
527 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
528 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
529 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
530
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
531 ## 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
532 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
533 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
534
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
535
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
536 ## 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
537
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
538 #if $pixel_output:
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
539 print("pixel list")
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
540 pixel_df = Reduce(function(...) merge(..., by=c("x", "y"), all=TRUE), spectrum_list)
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
541 write.table(pixel_df, file="$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
542 #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
543
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
544 ########################## 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
545
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
546 #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
547
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
548 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
549 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
550 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
551 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
552
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
553 #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
554
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
555 ################## 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
556 ############################################################################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
557 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
558 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
559
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
560 ########################## 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
561 ## 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
562
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
563 ## 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
564 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
565
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
566 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
567 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
568 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
569 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
570 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
571 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
572 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
573 }else{
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(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
575 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
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 }
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
578
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
579 ## 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
580
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
581 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
582 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
583 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
584 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
585
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
586 ## 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
587 ## 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
588 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
589
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
590 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
591 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
592
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
593 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
594 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
595 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
596 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
597 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
598 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
599 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
600 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
601 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
602 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
603
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
604 ########################## 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
605
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
606 ## 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
607 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
608
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
609 ## 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
610 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
611
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
612 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
613 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
614 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
615
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
616 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
617 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
618 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
619 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
620 }else{
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(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
622 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
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 }
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
625
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
626 ## 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
627 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
628 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
629 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
630 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
631
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
632 ## 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
633 ## 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
634 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
635 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
636 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
637
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
638 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
639 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
640 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
641 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
642 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
643 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
644 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
645 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
646 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
647 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
648
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
649 ################################## 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
650 ############################################################################
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
651 print("properties over m/z")
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
652
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
653 ########################## 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
654
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
655 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
656 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
657
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
658 ########################## 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
659
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
660 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
661
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
662 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
663 ## 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
664 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
665 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
666 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
667 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
668 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
669
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
670 ## 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
671 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
672 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
673 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
674 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
675
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
676 ########################## 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
677
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 ## 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
679 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
680
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
681 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
682 ## 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
683 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
684 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
685 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
686
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 ## 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
688 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
689 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
690 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
691 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
692 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
693
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
694 ################################## 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
695 ############################################################################
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
696 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
697 ########################## 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
698
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
699 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
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 ## 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
702 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
703
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
704 ## 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
705 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
706
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
707 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
708 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
709 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
710 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
711 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
712 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
713 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
714 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
715 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
716
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
717 ## 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
718 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
719 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
720 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
721 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
722 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
723
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
724 ## 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
725 ## 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
726 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
727
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
728 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
729 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
730 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
731 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
732 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
733 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
734 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
735 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
736
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 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
738 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
739 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
740 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
741 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
742 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
743 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
744 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
745 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
746 print(hist_13)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
747
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
748 ## 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
749 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
750
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
751 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
752 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
753 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
754 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
755
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
756 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
parents: 13
diff changeset
757 (axis(1, at = c(1:number_combined), labels=levels(msidata\$annotation), cex.axis=cex_boxplot, las=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
758 }
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
759
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
760 ################################## 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
parents: 10
diff changeset
761 ############################################################################
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
762 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
763
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
764 ############################ 15) Mass spectra ##############################
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
765
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
766 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
parents: 8
diff changeset
767 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
parents: 1
diff changeset
768 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
galaxyp
parents: 8
diff changeset
769 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
parents: 8
diff changeset
770 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
parents: 8
diff changeset
771 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
parents: 8
diff changeset
772
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
773 ################### 16) Zoomed in mass spectra for calibrants ##############
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
774
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
775 count = 1
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
776 differencevector = numeric()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
777 differencevector2 = vector()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
778
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
779 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
780
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
781 ### 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
782 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
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 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
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 ### 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
parents: 8
diff changeset
787 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
parents: 8
diff changeset
788 maxmasspixel = features(msidata, mz=inputcalibrantmasses[mass]+3)
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
789
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
790 ### 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
galaxyp
parents: 8
diff changeset
791 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
792
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
793 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
794 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
galaxyp
parents: 10
diff changeset
795 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
parents: 8
diff changeset
796 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
parents: 8
diff changeset
797 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
798 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
799 ppmdifference = NA
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
800 maxvalue = NA}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
801 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
802
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
803 ### 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
parents: 10
diff changeset
804 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
parents: 10
diff changeset
805 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
parents: 8
diff changeset
806 mzdifference2 = mzvalue - inputcalibrantmasses[mass]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
807 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
808 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
parents: 8
diff changeset
809
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
810 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
parents: 8
diff changeset
811 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
galaxyp
parents: 12
diff changeset
812 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
813 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
814 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
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diff changeset
815 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
parents: 12
diff changeset
816 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
parents: 9
diff changeset
817 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
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diff changeset
818 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
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diff changeset
819 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
820 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
parents: 9
diff changeset
821 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
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diff changeset
822 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
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diff changeset
823 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
824 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
825 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
826 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
827 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
828 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
829 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
830
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
831 ### 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
832
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
833 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
834 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
835 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
836 }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
837 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
838 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
839 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
840 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
841 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
842 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
843 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
844
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
845 ######### 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
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 ### 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
848
7
ae9d7703ff27 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 6
diff changeset
849 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
850 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
851
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
852 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
853 plot(0,type='n',axes=FALSE,ann=FALSE)
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
854 title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range")) ## here klammer weggenommen...
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
855 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
856
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
857 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
858 labs(title="Average m/z error (max. average intensity vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
859 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=16))+
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
860 geom_text(aes(label=differencevector), vjust=-0.3, size=5.5, col="blue") +
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
861 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=16))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
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 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
864 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
865
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
866 ######### 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
867
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
868 ### 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
869
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
870 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
871 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
872 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
873
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
874 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
875 labs(title="Average m/z error (closest measured m/z vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
876 theme(plot.title = element_text(hjust = 0.5, size=16))+theme(text=element_text(family="ArialMT", face="bold", size=16))+
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
877 geom_text(aes(label=differencevector2), vjust=-0.3, size=5.5, col="blue")+
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
878 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=16))
9
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 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
881
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
882 #################### 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
883
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
884 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
885 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
886 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
887 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
888 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
889 ### 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
890 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
891
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
892 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
893 ### 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
894 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
895 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
896 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
897
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
898 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
899 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
900
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
901 ### 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
902 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
903 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
904 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
905
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
906 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
907 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
908 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
909
14
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_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
911 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
912 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
913
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
914 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
915 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
916 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
917 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
918
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
919 ### 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
920 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
921
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
922 ## 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
923 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
924 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
925 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
926
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
927 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
928
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
929 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
930 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
931 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
932 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
933 }else{
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
934
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
935 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
936
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
937 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
938 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
939 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
940 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
941
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
942 }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
943 }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
944 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
945 }
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
946 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
947
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
948
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
949 ]]></configfile>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
950 </configfiles>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
951 <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
952 <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
953 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
954 <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
955 <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
956 <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
957 <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
958 </param>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
959 <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
960 <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
961 <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
962 <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
963 <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
964 <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
965 </param>
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>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
967 </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
968 <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
969 <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
970 <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
971 <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
972 </param>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
973 <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
974 <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
975 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
976 <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
977 <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
978 <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
979 </when>
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
980 <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
981 </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
982 <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
983 <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
984 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
985 <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
986 <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
987 <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
988 <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
989 <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
990 <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
991 <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
992 </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
993 <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
994 </inputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
995 <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
996 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "$infile.display_name QC_report"/>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
997 <data format="tabular" name="pixel_tabular_output" label="$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
998 <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
999 </data>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1000 </outputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1001 <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
1002 <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
1003 <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
1004 <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
1005 <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
1006 </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
1007 <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
1008 <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
1009 <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
1010 <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
1011 </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
1012 <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
1013 <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
1014 </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
1015 <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
1016 <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
1017 <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
1018 <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
1019 <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
1020 <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
1021 <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
1022 <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
1023 <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
1024 </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
1025 <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
1026 <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
1027 <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
1028 </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
1029
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1030 <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
1031 <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
1032 <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
1033 <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
1034 <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
1035 </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
1036 <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
1037 <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
1038 </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
1039 <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
1040 <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
1041 <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
1042 <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
1043 </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
1044
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
1045 <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
1046 <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
1047
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1048 <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
1049 <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
1050 <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
1051 <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
1052 <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
1053 <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
1054 </conditional>
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="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
1056 <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
1057 <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
1058 <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
1059 <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
1060 <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
1061 <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
1062 </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
1063 <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
1064 <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
1065 <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
1066 <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
1067 </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
1068 <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
1069 <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
1070 <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
1071 <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
1072 </test>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1073 </tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1074 <help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1075 <![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
1076 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
1077
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1078 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
1079
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1080 Input data: 3 types of input data can be used:
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1081
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 - 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
1083 - 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
1084 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .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
1085 - 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
1086
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1087 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
1088
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1089 - 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
1090 - 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
1091
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1092 Output:
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1093
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
1094 - 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
1095 - 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
1096
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1097 Tip:
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
1098
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1099 - 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
1100
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1101 ----------------------------------------------------------------------------------------------------------------------------------------------------
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1102
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1103 Overview of the QC report plots:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1104
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1105 - (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
1106 - (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
parents: 10
diff changeset
1107 - (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
1108 - 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
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 - 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
1111
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1112 x-y images (pixel/spectra information):
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1113
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1114 - (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
galaxyp
parents: 13
diff changeset
1115 - 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
galaxyp
parents: 10
diff changeset
1116 - (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
parents: 10
diff changeset
1117 - (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
1118 - (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
parents: 10
diff changeset
1119 - (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
parents: 10
diff changeset
1120 - 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
1121 - 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
1122 - 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
parents: 10
diff changeset
1123 - 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
1124
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1125 Properties over spectra/pixels:
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1126
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1127 - 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
1128 - (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
1129 - 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
parents: 13
diff changeset
1130 - (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
1131
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1132 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
1133
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1134 - 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
1135 - 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
1136 - 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
1137
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1138 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
1139
14
5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1140 - 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
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diff changeset
1141 - Log2-transformed intensities: Histogram of log2-transformed intensities.
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5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1142 - (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
1143 - (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.
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1144
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1145 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
1146
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1147 - 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
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1148 - (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.
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5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1149 - (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.
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1150 - (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
1151 - (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.
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5aad8ef93356 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 5bceedc3a11c950790692a4c64bbb83d46897bee
galaxyp
parents: 13
diff changeset
1152 - (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.
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
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1153
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1154
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1155 ]]>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1156 </help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1157 <citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1158 <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
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1159 </citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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1160 </tool>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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1161