Mercurial > repos > galaxyp > msi_qualitycontrol

annotate msi_qualitycontrol.xml @ 13:0a6923b31ed0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
author galaxyp
date Fri, 06 Jul 2018 14:11:55 -0400
parents d8e584de1e34
children 5aad8ef93356
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13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.4">
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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>
10
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11 <requirement type="package" version="0.5.0">r-scales</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code">
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14 <![CDATA[
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15 #if $infile.ext == 'imzml'
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16 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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17 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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18 #elif $infile.ext == 'analyze75'
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19 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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20 ln -s '${infile.extra_files_path}/img' infile.img &&
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21 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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22 #else
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23 ln -s '$infile' infile.RData &&
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24 #end if
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25 cat '${cardinal_qualitycontrol_script}' &&
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26 Rscript '${cardinal_qualitycontrol_script}'
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27 ]]>
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28 </command>
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29 <configfiles>
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30 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
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31
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32 ################################# load libraries and read file #################
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33
0
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34 library(Cardinal)
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35 library(ggplot2)
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36 library(RColorBrewer)
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37 library(gridExtra)
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38 library(KernSmooth)
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39 library(scales)
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40
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41
0
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42 #if $infile.ext == 'imzml'
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43 #if str($processed_cond.processed_file) == "processed":
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44 msidata <- readImzML('infile', mass.accuracy=$processed_cond.accuracy, units.accuracy = "$processed_cond.units")
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45 #else
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46 msidata <- readImzML('infile')
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47 #end if
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48 #elif $infile.ext == 'analyze75'
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49 msidata = readAnalyze('infile')
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50 #else
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51 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
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55 iData(msidata) <- iData(msidata)[]
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56
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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
0
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61 ###################################### file properties in numbers ######################
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62
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63 ## Number of features (m/z)
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64 maxfeatures = length(features(msidata))
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65 ## Range m/z
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66 minmz = round(min(mz(msidata)), digits=2)
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67 maxmz = round(max(mz(msidata)), digits=2)
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68 ## Number of spectra (pixels)
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69 pixelcount = length(pixels(msidata))
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70 ## Range x coordinates
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71 minimumx = min(coord(msidata)[,1])
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72 maximumx = max(coord(msidata)[,1])
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73 ## Range y coordinates
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74 minimumy = min(coord(msidata)[,2])
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75 maximumy = max(coord(msidata)[,2])
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76 ## Range of intensities
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77 minint = round(min(spectra(msidata)[], na.rm=TRUE), digits=2)
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78 maxint = round(max(spectra(msidata)[], na.rm=TRUE), digits=2)
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79 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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80 ## Number of intensities > 0
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81 npeaks= sum(spectra(msidata)[]>0, na.rm=TRUE)
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82 ## Spectra multiplied with m/z (potential number of peaks)
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83 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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84 ## Percentage of intensities > 0
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85 percpeaks = round(npeaks/numpeaks*100, digits=2)
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86 ## Number of empty TICs
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87 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
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88 NumemptyTIC = sum(TICs == 0)
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89 ## Median TIC
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90 medTIC = round(median(TICs), digits=2)
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91 ## Median peaks per spectrum
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92 medpeaks = median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE)
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93 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))
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94
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95 ## Processing informations
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96 processinginfo = processingData(msidata)
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97 centroidedinfo = processinginfo@centroided
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98
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99 ## if TRUE write processinginfo if FALSE write FALSE
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100
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101 ## normalization
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102 if (length(processinginfo@normalization) == 0) {
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103 normalizationinfo='FALSE'
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104 } else {
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105 normalizationinfo=processinginfo@normalization
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106 }
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107 ## smoothing
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108 if (length(processinginfo@smoothing) == 0) {
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109 smoothinginfo='FALSE'
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110 } else {
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111 smoothinginfo=processinginfo@smoothing
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112 }
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113 ## baseline
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114 if (length(processinginfo@baselineReduction) == 0) {
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115 baselinereductioninfo='FALSE'
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116 } else {
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117 baselinereductioninfo=processinginfo@baselineReduction
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118 }
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119 ## peak picking
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120 if (length(processinginfo@peakPicking) == 0) {
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121 peakpickinginfo='FALSE'
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122 } else {
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123 peakpickinginfo=processinginfo@peakPicking
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124 }
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125
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126 ############## Read and filter tabular file with m/z ###########################
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127
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128 ### reading calibrant file:
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129
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130 #if $calibrant_file:
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131
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132 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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133 if (ncol(calibrant_list) == 1)
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134 {calibrant_list = cbind(calibrant_list, calibrant_list)} ## if there is just one column dublicate it to have a names column
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135
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136 ### calculate how many input calibrant m/z are valid:
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137
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138 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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139 number_calibrants_in = length(calibrant_list[,1])
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140 number_calibrants_valid = length(inputcalibrants[,1])
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141
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142 #else
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143
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144 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
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145 number_calibrants_in = 0
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146 number_calibrants_valid = 0
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147
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148 #end if
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149
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150 ## rename input dataframe and extract m/z
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151 colnames(inputcalibrants) = c("m/z", "name")
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152 inputcalibrantmasses = inputcalibrants[,1]
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153
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154
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155 ######################################## PDF #############################################
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156 ##########################################################################################
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157 ##########################################################################################
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158
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159 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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160 plot(0,type='n',axes=FALSE,ann=FALSE)
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161
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162 ## if no filename is given, name of file in Galaxy history is used
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163
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164 #if not $filename:
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165 #set $filename = $infile.display_name
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166 #end if
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167
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168 title(main=paste("$filename"))
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169
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170 ################# I) file properties in numbers ################################
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171 ################################################################################
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172 print("properties in numbers")
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173
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174 properties = c("Number of m/z features",
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175 "Range of m/z values",
0
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176 "Number of pixels",
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177 "Range of x coordinates",
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178 "Range of y coordinates",
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179 "Range of intensities",
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180 "Median of intensities",
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181 "Intensities > 0",
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182 "Number of empty spectra",
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183 "Median TIC",
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184 "Median # peaks per spectrum",
0
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185 "Normalization",
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186 "Smoothing",
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187 "Baseline reduction",
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188 "Peak picking",
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189 "Centroided",
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190 paste0("calibrants (#valid/#input) in \n", "$calibrant_file.display_name"))
0
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191
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192 values = c(paste0(maxfeatures),
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193 paste0(minmz, " - ", maxmz),
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194 paste0(pixelcount),
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195 paste0(minimumx, " - ", maximumx),
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196 paste0(minimumy, " - ", maximumy),
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197 paste0(minint, " - ", maxint),
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198 paste0(medint),
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199 paste0(percpeaks, " %"),
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200 paste0(NumemptyTIC),
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201 paste0(medTIC),
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202 paste0(medpeaks),
0
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203 paste0(normalizationinfo),
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204 paste0(smoothinginfo),
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205 paste0(baselinereductioninfo),
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206 paste0(peakpickinginfo),
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207 paste0(centroidedinfo),
4
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208 paste0(number_calibrants_valid, " / ", number_calibrants_in))
0
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209
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210 property_df = data.frame(properties, values)
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211
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212 grid.table(property_df, rows= NULL)
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213
11
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214 ####################### II) x-y images #######################################
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215 ##############################################################################
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216 print("x-y images")
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217
13
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diff changeset
218 ## only do plots for file with intensity peaks
9
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219 if (npeaks > 0){
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220 ## function for density plots
2
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221 plot_colorByDensity = function(x1,x2,
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222 ylim=c(min(x2),max(x2)),
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223 xlim=c(min(x1),max(x1)),
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224 xlab="",ylab="",main=""){
4
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225 df = data.frame(x1,x2)
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226 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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227 df\$dens = col2rgb(x)[1,] + 1L
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228 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
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229 df\$col = cols[df\$dens]
9
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230 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
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231 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
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232
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diff changeset
233 abline_vector= -100000 ## will be filled for samples in case data is combined
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234
10
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235 ## start list for optional spectrum values output
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diff changeset
236 spectrum_list = list()
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diff changeset
237 list_count = 1
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238
9
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diff changeset
239 ################### 0) overview for combined data ###########################
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240
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diff changeset
241 ### only for previously combined data, same plot as in combine QC pdf
10
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242
9
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diff changeset
243 if (!is.null(levels(msidata\$combined_sample))){
10
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diff changeset
244 number_combined = length(levels(msidata\$combined_sample))
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245
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diff changeset
246 ## the more combined_samples a file has the smaller will be the legend
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diff changeset
247 if (number_combined<20){
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diff changeset
248 legend_size = 10
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diff changeset
249 cex_boxplot = 1
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diff changeset
250 }else if (number_combined>20 && number_combined<40){
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diff changeset
251 legend_size = 9
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252 cex_boxplot = 0.8
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253 }else if (number_combined>40 && number_combined<60){
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diff changeset
254 legend_size = 8
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diff changeset
255 cex_boxplot = 0.6
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256 }else if (number_combined>60 && number_combined<100){
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diff changeset
257 legend_size = 7
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diff changeset
258 cex_boxplot = 0.5
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diff changeset
259 }else{
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diff changeset
260 legend_size = 6
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261 cex_boxplot = 0.3
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262 }
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263
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264 position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
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265 colnames(position_df)[3] = "sample_name"
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266
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267 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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268 geom_tile() +
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269 coord_fixed()+
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270 ggtitle("Spatial orientation of combined data")+
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271 theme_bw()+
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272 theme(plot.title = element_text(hjust = 0.5))+
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273 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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274 theme(legend.position="bottom",legend.direction="vertical")+
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275 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
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276 guides(fill=guide_legend(ncol=5,byrow=TRUE))
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277 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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278 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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279 for(file_count in 1:nrow(coord_labels))
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280 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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281 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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282
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283 print(combine_plot)
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284
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285 ### find max pixelnumber per subsample to later draw ablines
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286 pixel_name_df = data.frame(pixels(msidata), msidata\$combined_sample)
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287 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
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288 last_pixel = aggregate(pixel_number~pixel_name, data = pixel_name_df, max)
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289 pixel_vector = last_pixel[,2]
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290 abline_vector = pixel_vector[1:number_combined-1]
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291 print(abline_vector)
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292 }
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293
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294 ################### 1) Pixel order image ###################################
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295
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296 pixelnumber = 1:pixelcount
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297 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
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298
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299 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+
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300 geom_tile() + coord_fixed()+
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301 ggtitle("Pixel order") + theme_bw()+
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302 theme(plot.title = element_text(hjust = 0.5))+
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303 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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304 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
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305 space = "Lab", na.value = "black", name = "Pixel\nnumber"))
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306
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307 ################ 2) Number of calibrants per spectrum ######################
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308
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309 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
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310 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
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311
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312 ## plot only possible when there is at least one valid calibrant
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313 if (length(inputcalibrantmasses) != 0){
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314
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315 ## calculate plusminus values in m/z for each calibrant
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316 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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317
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318 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
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319 for (mass in 1:length(inputcalibrantmasses)){
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320
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321 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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322
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323 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){
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324
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325 ## intensity of all m/z > 0
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326 intensity_sum = colSums(spectra(filtered_data)[], na.rm=TRUE) > 0
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327
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328 }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data)[], na.rm=TRUE) > 0){
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329
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330 ## intensity of only m/z > 0
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331 intensity_sum = spectra(filtered_data)[] > 0
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332
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333 }else{
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334 intensity_sum = rep(FALSE, ncol(filtered_data))}
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335
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336 ## for each pixel add sum of intensity in the given m/z range
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337 pixelmatrix = rbind(pixelmatrix, intensity_sum)
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338 }
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339
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340 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
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341 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
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342 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
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343 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
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344
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345 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+
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346 geom_tile() + coord_fixed() +
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347 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) +
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348 theme_bw() +
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349 theme(plot.title = element_text(hjust = 0.5))+
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350 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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351 scale_fill_manual(values = mycolours[1:length(countvector)],
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352 na.value = "black", name = "# calibrants"))
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353
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354 ## append list for optional tabular output with spectrum values
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355 colnames(countdf)[3] = "Number of Calibrants"
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356 spectrum_list[[list_count]] = countdf
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357 list_count = list_count+1
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358
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359 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
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360
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361 ########################## 3) fold change image ###########################
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362
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363 #if $calibrantratio:
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364 #for $foldchanges in $calibrantratio:
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365 mass1 = $foldchanges.mass1
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366 mass2 = $foldchanges.mass2
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367 distance = $foldchanges.distance
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368
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369 ### if user did not write a label use input m/z as label
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370 #if not str($foldchanges.filenameratioplot).strip():
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371 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
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372 #else:
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373 #set $label = $foldchanges.filenameratioplot
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374 #end if
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375
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376 ### filter msidata for given m/z range (for both input m/z)
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377 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,]
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378 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,]
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379
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380 ### find m/z in the two given ranges with the highest mean intensity
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381 ### this two m/z will be used to calculate the fold change (red line in plot)
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382 maxmassrow1 = rowMeans(spectra(filtered_data1), na.rm=TRUE)
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383 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)]
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384 maxmassrow2 = rowMeans(spectra(filtered_data2), na.rm=TRUE)
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385 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)]
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386
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387 ### plot legend: chosen value in blue, distance in blue, max m/z in red
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388 ### m/z range for each plot (fixed range of 5 Da)
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389 ### xlim does not work because it does not adjust for the max. intensities within the range
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390 mzdown1 = features(msidata, mz = mass1-2)
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391 mzup1 = features(msidata, mz = mass1+3)
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392 mzdown2 = features(msidata, mz = mass2-2)
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393 mzup2 = features(msidata, mz = mass2+3)
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394
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395 ### plot for first m/z
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396 par(mfrow=c(2,1), oma=c(0,0,2,0))
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397 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
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398 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,6,3))
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399 abline(v=maxmass1, col="red", lty=5)
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400
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401 ### plot for second m/z
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402 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
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403 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,6,3))
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404 abline(v=maxmass2, col="red", lty=5)
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405 title("Control of fold change plot", outer=TRUE)
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406
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407 ### filter spectra for max m/z to have two vectors, which can be divided
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408 ### plot spatial distribution of fold change
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409 ### only possible when there are intensities > 0 in both given m/z ranges
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410
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411 if (length(maxmass1)>0&length(maxmass2)>0){
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412 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),]
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413 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),]
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414 foldchange= log2(mass1vector/mass2vector)
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415 fcmatrix = cbind(foldchange, coord(msidata)[,1:2])
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416
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417 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange), colour=colo)+
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418 geom_tile() + coord_fixed()+
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419 ggtitle("$label")+
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420 theme_bw()+
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421 theme(plot.title = element_text(hjust = 0.5))+
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422 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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423 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
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diff changeset
424 ,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
425 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
426 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
427 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
428
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
429 #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
430 #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
431
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
432 #################### 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
433
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
434 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
435 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
436 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
437
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
438
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
439 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
parents: 10
diff changeset
440 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
441 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
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 } 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
444
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
445 #################### 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
446
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
447 ## 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
448 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
449 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
450
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
451 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
452 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
453 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
454 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
455 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
456 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
457 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
458 ,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
459
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
460 ## 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
461 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
462 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
463 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
464
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
465 ############################### 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
466
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
467 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
468 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
469 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
470 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
471 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
472 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
473 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
474 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
475 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
476 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
477 ,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
478
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
479 ## 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
480 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
481 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
482 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
483
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
484 ############################### 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
485
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
486 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
487 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
488 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
489
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
490 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
491 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
492 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
493 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
494 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
495 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
496 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
497 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
498
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
499 ## 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
500 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
501 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
502
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
503 ## 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
504
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
505 #if $pixel_output:
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
506 print("pixel list")
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
507 pixel_df = Reduce(function(...) merge(..., by=c("x", "y"), all=T), spectrum_list)
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
508 write.table(pixel_df, file="$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
509 #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
510
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
511 ########################## 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
512
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
513 #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
514
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
515 pca = PCA(msidata, ncomp=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
516 par(mfrow = c(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
517 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
518 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
519
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
520 #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
521
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
522 ################## III) properties over spectra index ##########
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
523 ##############################################################################
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
524 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
525 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
526
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
527 ########################## 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
528 ## 9a) scatterplot
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
529 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks 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
530 title(xlab="Spectra index", line=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
531 title(ylab="Number of peaks", 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
532 abline(v=abline_vector, lty = 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
533
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
534 ## 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
535
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
536 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
537 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
538 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
539 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
540
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
541 ## 9c) additional histogram to show subsample contributions
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
542 ## only when samples were combined before (combined_sample)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
543 if (!is.null(levels(msidata\$combined_sample))){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
544
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
545 df_9 = data.frame(peaksperpixel, msidata\$combined_sample)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
546 colnames(df_9) = c("Npeaks", "sample_name")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
547
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
548 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=sample_name)) +
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
549 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
550 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
551 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
552 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
553 theme(legend.position="bottom",legend.direction="vertical")+
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
554 labs(title="Number of peaks per spectrum and sample", 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
555 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
556 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
557 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
558
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
559 ########################## 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
560
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
561 ## 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
562 par(mfrow = c(2,1), mar=c(5,6,4,2))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
563 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC 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
564 title(xlab="Spectra index", line=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
565 title(ylab = "Total ion chromatogram intensity", 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
566 abline(v=abline_vector, lty = 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
567
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
568 ## 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
569 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
570 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
571 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
572 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
573
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
574 ## 10c) additional histogram to show subsample contributions
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
575 ## only when samples were combined before (combined_sample)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
576 if (!is.null(levels(msidata\$combined_sample))){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
577 df_10 = data.frame(log(TICs), msidata\$combined_sample)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
578 colnames(df_10) = c("TICs", "sample_name")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
579
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
580 hist_10 = ggplot(df_10, aes(x=TICs, fill=sample_name)) +
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
581 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
582 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
583 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
584 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
585 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = legend_size))+
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
586 labs(title="TIC per spectrum and sample", 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
587 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
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diff changeset
588 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
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diff changeset
589 print(hist_10)}
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
590
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
591 ################################## 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
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diff changeset
592 ############################################################################
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
593 print("propverties over 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
594
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
595 ########################## 11) Histogram on 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
596
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
597 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
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diff changeset
598 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
599
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
600 ########################## 12) Number of peaks per m/z #####################
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galaxyp
parents: 8
diff changeset
601
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
602 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
603
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
604 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
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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
605 ## 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
606 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
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diff changeset
607 title(xlab="m/z", line=2.5)
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4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
608 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
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diff changeset
609 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
610 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
611
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
612 ## 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
613 hist(peakspermz, main="", las=1, ylab="", xlab="")
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4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
614 title(ylab = "Frequency", line=4)
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
615 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
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diff changeset
616 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
617
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
618 ########################## 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
619
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
620 ## 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
621 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
622
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
623 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
624 ## 13a) scatterplot
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
625 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
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diff changeset
626 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
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diff changeset
627 title(ylab="Intensity sum", line=4)
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19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
628
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
629 ## 13b) histogram
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
630 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
631 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
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diff changeset
632 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
633 title(ylab = "Frequency", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
634 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
635
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
636 ################################## V) intensity plots ########################
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
637 ############################################################################
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
638 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
639 ########################## 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
640
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
641 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
642
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
643 ## 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
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diff changeset
644 medianint_spectra = apply(spectra(msidata), 2, median)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
645 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
646 title(ylab="Median spectrum intensity", line=4)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
647 abline(v=abline_vector, lty = 3)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
648
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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
649 ## 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
650 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
651 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
652 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
653 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
654 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
655
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
656 ## 14c) histogram to show subsample contribution
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
657 ## only for previously combined samples
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
658 if (!is.null(levels(msidata\$combined_sample))){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
659
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
660 df_13 = data.frame(matrix(,ncol=2, nrow=0))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
661 for (subsample in levels(msidata\$combined_sample)){
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
662 log2_int_subsample = log2(spectra(msidata)[,msidata\$combined_sample==subsample])
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
663 df_subsample = data.frame(as.numeric(log2_int_subsample))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
664 df_subsample\$sample_name = subsample
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
665 df_13 = rbind(df_13, df_subsample)}
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
666 df_13\$sample_name = as.factor(df_13\$sample_name)
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
667 colnames(df_13) = c("logint", "sample_name")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
668
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669 hist_13 = ggplot(df_13, aes(x=logint, fill=sample_name)) +
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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670 geom_histogram()+ theme_bw()+
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
671 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
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672 labs(title="Log2-transformed intensities per sample", x="log2 intensities", y = "Frequency") +
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673 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
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674 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
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675 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
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676 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
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677 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
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678 print(hist_13)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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679
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diff changeset
680 ## 14d) boxplots to visualize in a different way the intensity distributions
9
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diff changeset
681 par(mfrow = c(1,1), cex.axis=1.3, cex.lab=1.3, mar=c(13.1,4.1,5.1,2.1))
6
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682
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
683 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
684 for (subsample in levels(msidata\$combined_sample)){
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446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
685 mean_mz_sample = rowMeans(spectra(msidata)[,msidata\$combined_sample==subsample])
9
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diff changeset
686 mean_matrix = cbind(mean_matrix, mean_mz_sample)}
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446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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687
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
688 boxplot(log2(mean_matrix), ylab = "log2 mean intensity per m/z", main="Mean intensities per m/z and sample", xaxt = "n")
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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diff changeset
689 (axis(1, at = c(1:number_combined), labels=levels(msidata\$combined_sample), cex.axis=cex_boxplot, las=2))
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diff changeset
690 }
6
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691
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diff changeset
692 ################################## 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
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693 ############################################################################
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
694 print("Mass spectra and m/z accuracy")
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diff changeset
695
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
696 ############################ 15) Mass spectra ##############################
0
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diff changeset
697
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
698 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
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diff changeset
699 pixels_for_plot = c(round(length(pixelnumber)/2, , digits=0), round(length(pixelnumber)/4, , digits=0), round(length(pixelnumber)/4*3, , digits=0))
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diff changeset
700 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum")
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diff changeset
701 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
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diff changeset
702 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
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diff changeset
703 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
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diff changeset
704
13
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diff changeset
705 ################### 16) Zoomed in mass spectra for calibrants ##############
2
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parents: 1
diff changeset
706
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
707 count = 1
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
708 differencevector = numeric()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
709 differencevector2 = vector()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
710
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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parents: 8
diff changeset
711 if (length(inputcalibrantmasses) != 0){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
712
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
713 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots
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0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
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diff changeset
714 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses)) * inputcalibrantmasses
9
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parents: 8
diff changeset
715
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
716 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
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diff changeset
717
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
718 ### define the plot window with xmin und xmax
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
719 minmasspixel = features(msidata, mz=inputcalibrantmasses[mass]-1)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
720 maxmasspixel = features(msidata, mz=inputcalibrantmasses[mass]+3)
0
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diff changeset
721
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
722 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
723 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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diff changeset
724
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
725 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
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diff changeset
726 maxmassrow = rowMeans(spectra(filtered_data)) ## for each m/z average intensity is calculated
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
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diff changeset
727 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highest average intensity in m/z range
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
728 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
729 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
730 }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
731 ppmdifference = NA
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
732 maxvalue = NA}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
733 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
734
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
735 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18
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b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
736 mznumber = features(msidata, mz = inputcalibrantmasses[mass]) ### gives featurenumber which is closest to given m/z
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
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diff changeset
737 mzvalue = mz(msidata)[mznumber] ### gives closest m/z
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
738 mzdifference2 = mzvalue - inputcalibrantmasses[mass]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
739 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
740 differencevector2[mass] = round(ppmdifference2, digits=2)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
741
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
742 par(mfrow = c(2, 2), oma=c(0,0,2,0))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
743 plot(msidata[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "average spectrum")
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galaxyp
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diff changeset
744 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
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446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
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diff changeset
745 abline(v=c(maxvalue), col="red", lty=2)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
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parents: 9
diff changeset
746 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
747 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
748 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
749 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
750 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
751 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
752 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
753 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
754 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
755 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
756 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
757 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
758 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
759 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
760 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
761 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
762
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
763 ### 16b) one large extra plot with different colours for different samples (for combined_sample only)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
764
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
765 if (!is.null(levels(msidata\$combined_sample))){
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
766 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
767 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
768 }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
769 par(mfrow = c(1, 1))
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
770 plot(msidata[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata),main="Average spectrum per 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
771 pixel.groups=msidata\$combined_sample, key=key_zoomed, col=hue_pal()(number_combined),superpose=TRUE)
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
772 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
773 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
774 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
775 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
776
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
777 ######### 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
778
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
779 ### 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
780
7
ae9d7703ff27 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 6
diff changeset
781 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
782 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
783
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
784 if (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
785 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
786 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
787 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
788
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
789 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
790 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
791 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
792 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
793 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
794
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
795 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
796 }
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
797
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
798 ######### 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
799
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
800 ### 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
801
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
802 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
803 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
804 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
805
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
806 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
807 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
808 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
809 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
810 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
811
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 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
813
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
814
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
815 #################### 19) ppm difference over pixels #####################
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
816
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
817 par(mfrow = c(1,1))
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
818 mycolours = c("darkgrey", "darkblue", "blue", "green" , "red", "orange", "yellow", "magenta", "olivedrab1", "lightseagreen")
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
819 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
820 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata)))
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
821 for (calibrant in inputcalibrantmasses){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
822 ### find m/z with the highest mean intensity in m/z range, if no m/z in the range, all ppm differences will be NA
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
823 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
824
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
825 if (nrow(filtered_data) > 0){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
826 ### filtered for m/z range, now go through it pixel by pixel to find max peak in each spectrum
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
827 ppm_vector = numeric()
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
828 for (pixel_count in 1:ncol(filtered_data)){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
829 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])]
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
830
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
831 mzdiff = mz_max - calibrant
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
832 ppmdiff = mzdiff/calibrant*1000000
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
833
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
834 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
835 if (max(spectra(filtered_data)[,pixel_count]) == 0){
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
836 ppmdiff = NA}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
837 ppm_vector[pixel_count] = ppmdiff}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
838 }else{ppm_vector = rep(NA, ncol(msidata))}
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
839
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
840 ppm_df = cbind(ppm_df, ppm_vector)
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
841 count=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
842
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
843 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_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
844 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
845 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
846 }else{
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
847
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
848 ### plot ppm differences over pixels (spectra index)
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
849
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
850 par(mar=c(4.1, 4.1, 4.1, 7.5))
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
851 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)")
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
852
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 for (each_cal in 1:ncol(ppm_df)){
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
854 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
855 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
856 abline(v=abline_vector, lty = 3)}
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
857
13
0a6923b31ed0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 8087490eb4dcaf4ead0f03eae4126780d21e5503
galaxyp
parents: 12
diff changeset
858 }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
859 }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
860 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
861 }
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
862 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
863
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
864
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
865
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
866 ]]></configfile>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
867 </configfiles>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
868 <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
869 <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
870 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
871 <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
872 <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
873 <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
874 <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
875 </param>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
876 <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
877 <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
878 <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
879 <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
880 <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
881 <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
882 </param>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
883 </when>
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
884 </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
885 <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
886 <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
887 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
888 <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
889 <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
890 <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
891 <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
892 <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
893 <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
894 <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
895 </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
896 <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
897 </inputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
898 <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
899 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "$infile.display_name QC_report"/>
10
446fe0bb6320 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 37da74ed68228b16efbdbde776e7c38cc06eb5d5
galaxyp
parents: 9
diff changeset
900 <data format="tabular" name="pixel_tabular_output" label="$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
901 <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
902 </data>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
903 </outputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
904 <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
905 <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
906 <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
907 <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
908 <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
909 </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
910 <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
911 <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
912 <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
913 <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
914 </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
915 <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
916 <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
917 <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
918 <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
919 <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
920 <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
921 <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
922 <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
923 <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
924 </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
925 <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
926 <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
927 <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
928 </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
929 <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
930 <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
931 <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
932 <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
933 <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
934 </param>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
935 <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
936 <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
937 <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
938 <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
939 </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
940 <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
941 <param name="infile" value="123_combined.RData" ftype="rdata"/>
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
942 <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
943 <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
944 <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
945 <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
946 <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
947 </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
948 <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
949 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
950 <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
951 <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
952 <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
953 <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
954 </test>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
955 </tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
956 <help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
957 <![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
958 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
959
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
960 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
961
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
962 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
963
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
964 - 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
965 - 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
966 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
967
8
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
968 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
969
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
970 - 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
971 - 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
972
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
973 Output:
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
974
9
19e3a2f9d513 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
975 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
976 - optional spectra information as tabular file with 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
977
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
978 Tip:
42d010294f0b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
979
11
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
980 - 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
981
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
982 ----------------------------------------------------------------------------------------------------------------------------------------------------
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
983
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
984 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
985
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
986 - (comb): this plots will only be drawn if several files were combined into one file with the msi_combine tool
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
987 - (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
988 - (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
989 - 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
990
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
991 - 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
992
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
993 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
994
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
995 - (comb) Spatial orientation of combined data: All pixels of a combined file have the same colour.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
996 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
997 - (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
998 - (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
999 - (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
1000 - (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
1001 - 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
1002 - 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
1003 - 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
1004 - 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
1005
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1006 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
1007
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1008 - Number of peaks per spectrum: Scatter plot and histogram showing the number of intensities > 0 for each spectrum. Dotted lines in the scatter plot separate spectra of combined samples.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1009 - (comb) Number of peaks per spectrum and sample: Same histogram as in plot before but with colours to show the contribution of each combined sample.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1010 - 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 combined samples.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1011 - (comb) TIC per spectrum and sample: Same histogram as in plot before but with colours to show the contribution of each combined sample.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1012
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1013 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
1014
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1015 - 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
1016 - 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
1017 - 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
1018
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1019 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
1020
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1021 - 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 combined samples.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1022 - Log2-transformed intensities: Histogram of log2-transformed intensities.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1023 - (comb) log2-transformed intensities per sample: Same histogram as before but with colours to show the contribution of each combined sample.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1024 - (comb) Mean intensities per m/z and sample: For all pixels of a sample the mean intensity for each m/z is calculated and shown as boxplot.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1025
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1026 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
1027
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1028 - Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from single pixels (spectra).
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1029 - (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.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1030 - (comb) Average spectrum per sample: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each combined sample separately.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1031 - (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
1032 - (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.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1033 - (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 combined samples.
b3fbaf973cfd planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 6d877681b6188999b4f5abb1843b420078b71b92
galaxyp
parents: 10
diff changeset
1034
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1035
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1036 ]]>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1037 </help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1038 <citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1039 <citation type="doi">10.1093/bioinformatics/btv146</citation>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1040 </citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
1041 </tool>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
1042