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annotate msi_qualitycontrol.xml @ 9:963c7ec00141 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
author galaxyp
date Mon, 11 Jun 2018 17:34:19 -0400
parents 52ef77866de8
children 3eee933c27cf
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9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.10.0.1">
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2 <description>
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3 mass spectrometry imaging QC
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.10.0">bioconductor-cardinal</requirement>
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7 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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8 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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9 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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10 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code">
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13 <![CDATA[
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14 #if $infile.ext == 'imzml'
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15 ln -s '${infile.extra_files_path}/imzml' infile.imzML &&
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16 ln -s '${infile.extra_files_path}/ibd' infile.ibd &&
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17 #elif $infile.ext == 'analyze75'
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18 ln -s '${infile.extra_files_path}/hdr' infile.hdr &&
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19 ln -s '${infile.extra_files_path}/img' infile.img &&
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20 ln -s '${infile.extra_files_path}/t2m' infile.t2m &&
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21 #else
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22 ln -s '$infile' infile.RData &&
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23 #end if
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24 cat '${cardinal_qualitycontrol_script}' &&
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25 Rscript '${cardinal_qualitycontrol_script}'
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26 ]]>
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27 </command>
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28 <configfiles>
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29 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
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30
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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31 ################################# load libraries and read file #################
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32
0
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33 library(Cardinal)
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34 library(ggplot2)
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35 library(RColorBrewer)
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36 library(gridExtra)
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37 library(KernSmooth)
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38
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39 #if $infile.ext == 'imzml'
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40 msidata = readImzML('infile')
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41 #elif $infile.ext == 'analyze75'
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42 msidata = readAnalyze('infile')
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43 #else
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44 load('infile.RData')
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45 #end if
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46
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47 ###################################### file properties in numbers ######################
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48
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49 ## Number of features (m/z)
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50 maxfeatures = length(features(msidata))
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51 ## Range m/z
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52 minmz = round(min(mz(msidata)), digits=2)
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53 maxmz = round(max(mz(msidata)), digits=2)
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54 ## Number of spectra (pixels)
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55 pixelcount = length(pixels(msidata))
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56 ## Range x coordinates
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57 minimumx = min(coord(msidata)[,1])
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58 maximumx = max(coord(msidata)[,1])
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59 ## Range y coordinates
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60 minimumy = min(coord(msidata)[,2])
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61 maximumy = max(coord(msidata)[,2])
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62 ## Range of intensities
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63 minint = round(min(spectra(msidata)[]), digits=2)
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64 maxint = round(max(spectra(msidata)[]), digits=2)
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65 medint = round(median(spectra(msidata)[]), digits=2)
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66 ## Number of intensities > 0
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67 npeaks= sum(spectra(msidata)[]>0)
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68 ## Spectra multiplied with m/z (potential number of peaks)
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69 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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70 ## Percentage of intensities > 0
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71 percpeaks = round(npeaks/numpeaks*100, digits=2)
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72 ## Number of empty TICs
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73 TICs = colSums(spectra(msidata)[])
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74 NumemptyTIC = sum(TICs == 0)
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75 ## Median TIC
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76 medTIC = median(TICs)
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77 ## Median peaks per spectrum
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78 medpeaks = median(colSums(spectra(msidata)[]>0))
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79 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))
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80
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81 ## Processing informations
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82 processinginfo = processingData(msidata)
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83 centroidedinfo = processinginfo@centroided
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84
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85 ## if TRUE write processinginfo if FALSE write FALSE
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86
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87 ## normalization
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88 if (length(processinginfo@normalization) == 0) {
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89 normalizationinfo='FALSE'
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90 } else {
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91 normalizationinfo=processinginfo@normalization
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92 }
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93 ## smoothing
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94 if (length(processinginfo@smoothing) == 0) {
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95 smoothinginfo='FALSE'
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96 } else {
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97 smoothinginfo=processinginfo@smoothing
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98 }
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99 ## baseline
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100 if (length(processinginfo@baselineReduction) == 0) {
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101 baselinereductioninfo='FALSE'
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102 } else {
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103 baselinereductioninfo=processinginfo@baselineReduction
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104 }
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105 ## peak picking
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106 if (length(processinginfo@peakPicking) == 0) {
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107 peakpickinginfo='FALSE'
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108 } else {
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109 peakpickinginfo=processinginfo@peakPicking
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110 }
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111
9
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112
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113 ############## Read and filter tabular file with m/z ###########################
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114
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115 ### reading peptide file:
4
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116
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117 #if $peptide_file:
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118
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119 input_list = read.delim("$peptide_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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120 if (ncol(input_list) == 1)
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121 {input_list = cbind(input_list, input_list)} ## if there is just one column dublicate it to have a names column
4
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122
9
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123 ### calculate how many input peptide m/z are valid:
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124
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125 inputpeptides = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
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126 number_peptides_in = length(input_list[,1])
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127 number_peptides_valid = length(inputpeptides[,1])
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128
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129 #else
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130
5
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131 inputpeptides = as.data.frame(matrix(, nrow = 0, ncol = 2))
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132 number_peptides_in = 0
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133 number_peptides_valid = 0
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134
4
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135 #end if
2
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136
9
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137 colnames(inputpeptides) = c("m/z", "name")
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138
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139 ### reading calibrant file:
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140
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141 #if $calibrant_file:
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142
4
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143 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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144 if (ncol(calibrant_list) == 1)
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145 {calibrant_list = cbind(calibrant_list, calibrant_list)} ## if there is just one column dublicate it to have a names column
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146
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147 ### calculate how many input calibrant m/z are valid:
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148
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149 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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150 number_calibrants_in = length(calibrant_list[,1])
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151 number_calibrants_valid = length(inputcalibrants[,1])
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152
4
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153 #else
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154
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155 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
4
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156 number_calibrants_in = 0
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157 number_calibrants_valid = 0
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158
4
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159 #end if
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160
9
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161 colnames(inputcalibrants) = c("m/z", "name")
0
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162
9
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163 ### bind inputcalibrants and inputpeptides together, to make m/z heatmaps on both
2
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164
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165 inputs_all = rbind(inputcalibrants[,1:2], inputpeptides[,1:2])
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166 inputmasses = inputs_all[,1]
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167 inputnames = inputs_all[,2]
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168
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169 ######################################## PDF #############################################
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170 ##########################################################################################
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171 ##########################################################################################
0
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172
9
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173 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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174 plot(0,type='n',axes=FALSE,ann=FALSE)
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175
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176 ## if no filename is given, name of file in Galaxy history is used
5
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177
9
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178 #if not $filename:
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179 #set $filename = $infile.display_name
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180 #end if
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181
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182 title(main=paste("$filename"))
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183
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184 ################# I) file properties in numbers ################################
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185 ################################################################################
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186 print("properties in numbers")
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187
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188 properties = c("Number of m/z features",
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189 "Range of m/z values [Da]",
0
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190 "Number of pixels",
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191 "Range of x coordinates",
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192 "Range of y coordinates",
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193 "Range of intensities",
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194 "Median of intensities",
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195 "Intensities > 0",
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196 "Number of zero TICs",
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197 "Median TIC",
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198 "Median # peaks per spectrum",
0
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199 "Normalization",
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200 "Smoothing",
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201 "Baseline reduction",
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202 "Peak picking",
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203 "Centroided",
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204 paste0("# peptides in \n", "$peptide_file.display_name"),
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205 paste0("# calibrants in \n", "$calibrant_file.display_name"))
0
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206
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207 values = c(paste0(maxfeatures),
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208 paste0(minmz, " - ", maxmz),
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209 paste0(pixelcount),
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210 paste0(minimumx, " - ", maximumx),
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211 paste0(minimumy, " - ", maximumy),
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212 paste0(minint, " - ", maxint),
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213 paste0(medint),
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214 paste0(percpeaks, " %"),
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215 paste0(NumemptyTIC),
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216 paste0(medTIC),
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217 paste0(medpeaks),
0
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218 paste0(normalizationinfo),
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219 paste0(smoothinginfo),
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220 paste0(baselinereductioninfo),
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221 paste0(peakpickinginfo),
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222 paste0(centroidedinfo),
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223 paste0(number_peptides_valid, " / " , number_peptides_in),
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224 paste0(number_calibrants_valid, " / ", number_calibrants_in))
0
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225
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226
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227 property_df = data.frame(properties, values)
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228
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229 grid.table(property_df, rows= NULL)
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230
9
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231 ####################### II) images in x-y grid ###############################
2
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232 ##############################################################################
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233 print("x-y images")
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234 if (npeaks > 0){
0
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235
9
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236 ## function for density plots
2
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237 plot_colorByDensity = function(x1,x2,
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238 ylim=c(min(x2),max(x2)),
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239 xlim=c(min(x1),max(x1)),
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240 xlab="",ylab="",main=""){
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241 df = data.frame(x1,x2)
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242 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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243 df\$dens = col2rgb(x)[1,] + 1L
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244 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
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245 df\$col = cols[df\$dens]
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246 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
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247 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
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248
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249 abline_vector= -100000 ## will be filled for samples in case data is combined
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250
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251 ################### 0) overview for combined data ###########################
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252
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253 ### only for previously combined data, same plot as in combine QC pdf
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254 if (!is.null(levels(msidata\$combined_sample))){
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255 position_df = cbind(coord(msidata)[,1:2], msidata\$combined_sample)
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256 colnames(position_df)[3] = "sample_name"
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257
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258 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=sample_name))+
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259 geom_tile() +
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260 coord_fixed()+
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261 ggtitle("Spatial orientation of combined data")+
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262 theme_bw()+
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263 theme(text=element_text(family="ArialMT", face="bold", size=15))+
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264 theme(legend.position="bottom",legend.direction="vertical")+
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265 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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266 coord_labels = aggregate(cbind(x,y)~sample_name, data=position_df, mean)
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267 coord_labels\$file_number = gsub( "_.*$", "", coord_labels\$sample_name)
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268 for(file_count in 1:nrow(coord_labels))
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269 {combine_plot = combine_plot + annotate("text",x=coord_labels[file_count,"x"],
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270 y=coord_labels[file_count,"y"],label=toString(coord_labels[file_count,4]))}
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271 print(combine_plot)
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272
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273 ### find max pixelnumber per subsample to later draw ablines
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274 pixel_name_df = data.frame(pixels(msidata), msidata\$combined_sample)
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275 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
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276 last_pixel = aggregate(pixel_number~pixel_name, data = pixel_name_df, max)
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277 pixel_vector = last_pixel[,2]
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278 abline_vector = pixel_vector[1:length(levels(msidata\$combined_sample))-1]
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279 print(abline_vector)
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280 }
0
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281
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282
9
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283 ################### 1) Pixel order image ###################################
2
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284
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285 pixelnumber = 1:pixelcount
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286 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
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287
2
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288 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))
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289 + geom_tile() + coord_fixed()
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290 + ggtitle("Pixel order")
2
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291 +theme_bw()
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292 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
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293 space = "Lab", na.value = "black", name = "Acq"))
2
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294
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295 ################ 2) Number of calibrants per spectrum ######################
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296
2
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297 pixelmatrix = matrix(ncol=ncol(msidata), nrow=0)
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298 inputcalibrantmasses = inputcalibrants[,1]
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299
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300 ### find m/z range (ppm) for each calibrant and extract intensity matrix for this range
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301 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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302
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303 if (length(inputcalibrantmasses) != 0){
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304 for (calibrantnr in 1:length(inputcalibrantmasses)){
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305 calibrantmz = inputcalibrantmasses[calibrantnr]
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306 calibrantfeaturemin = features(msidata, mz=calibrantmz-plusminusvalues[calibrantnr])
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307 calibrantfeaturemax = features(msidata, mz=calibrantmz+plusminusvalues[calibrantnr])
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308
9
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309 ## in case m/z range includes only 1 m/z:
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310 if (calibrantfeaturemin == calibrantfeaturemax){
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311 calibrantintensity = spectra(msidata)[calibrantfeaturemin,]
2
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312 }else{
9
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313 ## if m/z range includes more than 1 m/z take sum of intensities
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314 calibrantintensity = colSums(spectra(msidata)[calibrantfeaturemin:calibrantfeaturemax,])
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315 }
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316 ## for each pixel add sum of intensity in the given m/z range
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317 pixelmatrix = rbind(pixelmatrix, calibrantintensity)
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318 }
0
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319
2
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320 countvector= as.factor(colSums(pixelmatrix>0))
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321 countdf= cbind(coord(msidata)[,1:2], countvector)
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322 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
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323
2
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324 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))
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325 + geom_tile() + coord_fixed()
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326 + ggtitle("Number of calibrants per pixel")
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327 + theme_bw()
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328 + theme(text=element_text(family="ArialMT", face="bold", size=12))
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329 + scale_fill_manual(values = mycolours[1:length(countvector)],
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330 na.value = "black", name = "# calibrants"))
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331 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
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332
9
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333 ########################## 3) fold change image ###########################
2
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334
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335 #if $calibrantratio:
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336 #for $foldchanges in $calibrantratio:
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337 mass1 = $foldchanges.mass1
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338 mass2 = $foldchanges.mass2
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339 distance = $foldchanges.distance
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340
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341 ### if user did not write a label use input m/z as label
3
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342 #if not str($foldchanges.filenameratioplot).strip():
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343 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
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344 #else:
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345 #set $label = $foldchanges.filenameratioplot
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346 #end if
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347
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348 ### filter msidata for given m/z range (for both input m/z)
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349 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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350 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,]
0
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351
9
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352 ### find m/z in the two given ranges with the highest mean intensity
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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353 ### this two m/z will be used to calculate the fold change (red line in plot)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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354 maxmassrow1 = rowMeans(spectra(filtered_data1))
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355 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)]
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356 maxmassrow2 = rowMeans(spectra(filtered_data2))
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357 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)]
2
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358
9
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359 ### plot legend: chosen value in blue, distance in blue, max m/z in red
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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360 ### m/z range for each plot (fixed range of 5 Da)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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361 ### xlim does not work because it does not adjust for the max. intensities within the range
2
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362 mzdown1 = features(msidata, mz = mass1-2)
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363 mzup1 = features(msidata, mz = mass1+3)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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364 mzdown2 = features(msidata, mz = mass2-2)
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365 mzup2 = features(msidata, mz = mass2+3)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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366
9
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367 ### plot for first m/z
2
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368 par(mfrow=c(2,1), oma=c(0,0,2,0))
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369 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
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370 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,6,3))
2
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371 abline(v=maxmass1, col="red", lty=5)
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372
9
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373 ### plot for second m/z
2
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374 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
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375 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,6,3))
2
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376 abline(v=maxmass2, col="red", lty=5)
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377 title("Control of fold change plot", outer=TRUE)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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378
9
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379 ### filter spectra for max m/z to have two vectors, which can be divided
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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380 ### plot spatial distribution of fold change
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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381 ### only possible when there are intensities > 0 in both given m/z ranges
2
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382
9
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383 if (length(maxmass1)>0&length(maxmass2)>0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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384 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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385 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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386 foldchange= log2(mass1vector/mass2vector)
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387 fcmatrix = cbind(foldchange, coord(msidata)[,1:2])
0
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388
9
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389 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange), colour=colo)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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390 + geom_tile() + coord_fixed()
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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391 + ggtitle("$label")
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392 + theme_bw()
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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393 + theme(text=element_text(family="ArialMT", face="bold", size=12))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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394 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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395 ,space = "Lab", na.value = "black", name ="FC"))
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diff changeset
396 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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397 plot(0,type='n',axes=FALSE,ann=FALSE)
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398 title(main=paste("At least one m/z range did not contain any intensity value > 0,\n therefore no foldchange plot could be drawn"))}
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diff changeset
399
2
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diff changeset
400 #end for
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diff changeset
401 #end if
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402
9
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403 #################### 4) m/z heatmaps #######################################
2
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diff changeset
404
3
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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diff changeset
405 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
9
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diff changeset
406 if (length(inputmasses) != 0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
407 for (mass in 1:length(inputmasses)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
408 image(msidata, mz=inputmasses[mass], plusminus=$plusminus_dalton,
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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409 main= paste0(inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"),
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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410 contrast.enhance = "histogram")
2
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diff changeset
411 }
9
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diff changeset
412 } else {print("4) The input peptide and calibrant m/z were not provided or outside the m/z range")}
2
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diff changeset
413
9
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diff changeset
414 #################### 5) Number of peaks per pixel - image ##################
2
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galaxyp
parents: 1
diff changeset
415
9
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diff changeset
416 ## here every intensity value > 0 counts as pixel
2
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417 peaksperpixel = colSums(spectra(msidata)[]> 0)
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
418 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel)
2
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galaxyp
parents: 1
diff changeset
419
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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420 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)
9
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diff changeset
421 + geom_tile() + coord_fixed()
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
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diff changeset
422 + ggtitle("Number of peaks per spectrum")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
423 + theme_bw()
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
424 + theme(text=element_text(family="ArialMT", face="bold", size=12))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
425 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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426 ,space = "Lab", na.value = "black", name = "# peaks"))
0
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galaxyp
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diff changeset
427
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
428 ############################### 6) TIC image ###############################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
429
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
430 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
431 colo = colorRampPalette(
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
432 c("blue", "cyan", "green", "yellow","red"))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
433 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
434 + geom_tile() + coord_fixed()
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
435 + ggtitle("Total Ion Chromatogram")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
436 + theme_bw()
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
437 + theme(text=element_text(family="ArialMT", face="bold", size=12))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
438 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
439 ,space = "Lab", na.value = "black", name = "TIC"))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
440
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
441 ############################### 7) Most abundant m/z image #################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
442
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
443 highestmz = apply(spectra(msidata)[],2,which.max)
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
444 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz])
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
445 colnames(highestmz_matrix)[3] = "highestmzinDa"
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
446
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
447 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
448 + geom_tile() + coord_fixed()
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
449 + ggtitle("Most abundant m/z in each spectrum")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
450 + theme_bw()
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
451 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z",
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
452 labels = as.character(pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)]),
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
453 breaks = pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)], limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
454 + theme(text=element_text(family="ArialMT", face="bold", size=12)))
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
455
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
456 ## which m/z are highest
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
457 highestmz_peptides = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[1])
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
458 highestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == highestmz_peptides)[1]
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
459
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
460 secondhighestmz = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[2])
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
461 secondhighestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == secondhighestmz)[1]
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
462
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
463 print(head(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
464
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
465 ########################## 8) pca image for two components #################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
466
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
467 pca = PCA(msidata, ncomp=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
468 par(mfrow = c(2,1))
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
469 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
470 image(pca, col=c("black", "white"), strip=FALSE)
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
471
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
472 ################## III) properties over spectra index ##########
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
473 ##############################################################################
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
474 print("properties over pixels")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
475 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
476
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
477 ########################## 9) number of peaks per spectrum #################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
478 ## 9a) scatterplot
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
479 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
480 title(xlab="Spectra index", line=3)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
481 title(ylab="Number of peaks", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
482 abline(v=abline_vector, lty = 3)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
483
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
484 ## 9b) histogram
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
485
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
486 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
487 title(main="Number of peaks per spectrum", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
488 title(ylab="Frequency = # spectra", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
489 abline(v=median(peaksperpixel), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
490
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
491 ## 9c) additional histogram to show subsample contributions
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
492 ## only when samples were combined before (combined_sample)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
493 if (!is.null(levels(msidata\$combined_sample))){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
494
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
495 df_9 = data.frame(peaksperpixel, msidata\$combined_sample)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
496 colnames(df_9) = c("Npeaks", "sample_name")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
497
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
498 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=sample_name)) +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
499 geom_histogram()+ theme_bw()+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
500 theme(text=element_text(family="ArialMT", face="bold", size=12))+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
501 labs(title="Number of peaks per spectrum and sample", x="Number of peaks per spectrum", y = "Frequency = # spectra") +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
502 geom_vline(xintercept = median(peaksperpixel), size = 1, colour = "black",linetype = "dashed")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
503 print(hist_9)}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
504
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
505 ########################## 10) TIC per spectrum ###########################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
506
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
507 ## 10a)density scatterplot
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
508 par(mfrow = c(2,1), mar=c(5,6,4,2))
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
509 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
510 title(xlab="Spectra index", line=3)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
511 title(ylab = "Total ion chromatogram intensity", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
512 abline(v=abline_vector, lty = 3)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
513
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
514 ## 10b) histogram
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
515 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
516 title(main= "TIC per spectrum", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
517 title(ylab="Frequency = # spectra", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
518 abline(v=median(log(TICs[TICs>0])), col="blue")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
519
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
520 ## 10c) additional histogram to show subsample contributions
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
521 ## only when samples were combined before (combined_sample)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
522 if (!is.null(levels(msidata\$combined_sample))){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
523 df_10 = data.frame(log(TICs), msidata\$combined_sample)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
524 colnames(df_10) = c("TICs", "sample_name")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
525
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
526 hist_10 = ggplot(df_10, aes(x=TICs, fill=sample_name)) +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
527 geom_histogram()+ theme_bw()+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
528 theme(text=element_text(family="ArialMT", face="bold", size=12))+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
529 labs(title="TIC per spectrum and sample", x="log(TIC per spectrum)", y = "Frequency = # spectra") +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
530 geom_vline(xintercept = median(log(TICs[TICs>0])), size = 1, colour = "black",linetype = "dashed")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
531 print(hist_10)}
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
532
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
533 ################################## IV) changes over m/z ####################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
534 ############################################################################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
535 print("changes over m/z")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
536 ########################## 11) Number of peaks per m/z #####################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
537
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
538 peakspermz = rowSums(spectra(msidata)[] > 0 )
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
539
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
540 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
541 ## 11a) scatterplot
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
542 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per m/z", ylab ="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
543 title(xlab="m/z", line=2.5)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
544 title(ylab = "Number of peaks", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
545 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
546 mtext("Coverage of spectra [%]", 4, line=3, adj=1)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
547
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
548 ## 11b) histogram
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
549 hist(peakspermz, main="", las=1, ylab="", xlab="")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
550 title(ylab = "Frequency", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
551 title(main="Number of peaks per m/z", xlab = "Number of peaks per m/z", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
552 abline(v=median(peakspermz), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
553
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
554 ########################## 12) Sum of intensities per m/z ##################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
555
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
556 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
557 mzTIC = rowSums(spectra(msidata)[]) ## calculate intensity sum for each m/z
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
558
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
559 par(mfrow = c(2,1), mar=c(5,6,4,2))
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
560 ## 12a) scatterplot
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
561 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per m/z", ylab ="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
562 title(xlab="m/z", line=2.5)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
563 title(ylab="Intensity sum", line=4)
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
564
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
565 ## 12b) histogram
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
566 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
567 title(main="Sum of intensities per m/z", line=2, ylab="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
568 title(xlab = "log (sum of intensities per m/z)")
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
569 title(ylab = "Frequency", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
570 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
571
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
572 ################################## V) general plots ########################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
573 ############################################################################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
574 print("general plots")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
575 ########################## 13) Intensity distribution ######################
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
576
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
577 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
578
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
579 ## 13a) Median intensity over spectra
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
580 medianint_spectra = apply(spectra(msidata), 2, median)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
581 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
582 title(ylab="Median spectrum intensity", line=4)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
583 abline(v=abline_vector, lty = 3)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
584
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
585 ## 13b) histogram:
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
586 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
587 title(main="Log2-transformed intensities", line=2)
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
588 title(xlab="log2 intensities")
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
589 title(ylab="Frequency", line=4)
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
590 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)])), col="blue")
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
591
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
592 ## 13c) histogram to show subsample contribution
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
593 ## only for previously combined samples
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594 if (!is.null(levels(msidata\$combined_sample))){
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595
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596 df_13 = data.frame(matrix(,ncol=2, nrow=0))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
597 for (subsample in levels(msidata\$combined_sample)){
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598 log2_int_subsample = log2(spectra(msidata)[,msidata\$combined_sample==subsample])
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599 df_subsample = data.frame(as.numeric(log2_int_subsample))
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600 df_subsample\$sample_name = subsample
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601 df_13 = rbind(df_13, df_subsample)}
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602 df_13\$sample_name = as.factor(df_13\$sample_name)
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603 colnames(df_13) = c("logint", "sample_name")
2
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604
9
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605 hist_13 = ggplot(df_13, aes(x=logint, fill=sample_name)) +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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606 geom_histogram()+ theme_bw()+
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607 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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608 labs(title="Log2-transformed intensities per sample", x="log2 intensities", y = "Frequency") +
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609 geom_vline(xintercept = median(log2(spectra(msidata)[(spectra(msidata)>0)])), size = 1, colour = "black",linetype = "dashed")
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610 print(hist_13)
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611
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diff changeset
612 ## 13d) boxplots to visualize in a different way the intensity distributions
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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613 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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614
9
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615 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata))
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616 for (subsample in levels(msidata\$combined_sample)){
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617 mean_mz_sample = colMeans(spectra(msidata)[,msidata\$combined_sample==subsample])
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618 mean_matrix = cbind(mean_matrix, mean_mz_sample)}
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619 boxplot(mean_matrix, ylab = "mean intensity per m/z", names=levels(msidata\$combined_sample), main="Mean intensities per m/z and sample", las=2)
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diff changeset
620 }
6
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621
9
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622 ########################## 14) Histogram on m/z values #####################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
623
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624 par(mfrow = c(1, 1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
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625 hist(mz(msidata), xlab = "m/z", main="Histogram of m/z values")
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626
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diff changeset
627 ############################ 15) Mass spectra ##############################
0
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628
2
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629 par(mfrow = c(2, 2))
9
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630 pixels_for_plot = c(round(length(pixelnumber)/2, , digits=0), round(length(pixelnumber)/4, , digits=0), round(length(pixelnumber)/4*3, , digits=0))
2
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631 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum")
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632 plot(msidata, pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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633 plot(msidata, pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2])))
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634 plot(msidata, pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2])))
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635
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diff changeset
636 #################### 16) Zoomed in mass spectra for calibrants##############
2
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637
9
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diff changeset
638 count = 1
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639 differencevector = numeric()
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diff changeset
640 differencevector2 = vector()
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641
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diff changeset
642 if (length(inputcalibrantmasses) != 0){
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diff changeset
643
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diff changeset
644 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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645 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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646
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diff changeset
647 for (mass in 1:length(inputcalibrantmasses)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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648
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diff changeset
649 ### define the plot window with xmin und xmax
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650 minmasspixel = features(msidata, mz=inputcalibrantmasses[mass]-1)
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651 maxmasspixel = features(msidata, mz=inputcalibrantmasses[mass]+3)
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diff changeset
652
9
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653 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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654 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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655 if (nrow(filtered_data) > 0 & sum(spectra(filtered_data)) > 0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
656 maxmassrow = rowMeans(spectra(filtered_data))
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diff changeset
657 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highestaverage intensity in m/z range
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diff changeset
658 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value
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diff changeset
659 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement
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diff changeset
660 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
661 ppmdifference = NA
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662 maxvalue = NA}
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663 differencevector[mass] = round(ppmdifference, digits=2)
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664
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diff changeset
665 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18
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diff changeset
666 mznumber = features(msidata, mz = inputcalibrantmasses[mass]) ### gives closest featurenumber which is closest to given m/z
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667 mzvalue = mz(msidata)[mznumber] ### gives the closest m/z
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668 mzdifference2 = mzvalue - inputcalibrantmasses[mass]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
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diff changeset
669 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000
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diff changeset
670 differencevector2[mass] = round(ppmdifference2, digits=2)
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diff changeset
671
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diff changeset
672 par(mfrow = c(2, 2), oma=c(0,0,2,0))
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673 plot(msidata[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "average spectrum")
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diff changeset
674 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,6,3))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
675 abline(v=c(maxvalue), col="red", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
676 abline(v=c(mzvalue), col="green2", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
677 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[1], main=paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[1],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
678 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,6,3))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
679 abline(v=c(maxvalue), col="red", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
680 abline(v=c(mzvalue), col="green2", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
681 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[2], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[2],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
682 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,6,3))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
683 abline(v=c(maxvalue), col="red", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
684 abline(v=c(mzvalue), col="green2", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
685 plot(msidata[minmasspixel:maxmasspixel,], pixel = pixels_for_plot[3], main= paste0("Spectrum at ", rownames(coord(msidata)[pixels_for_plot[3],1:2])))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
686 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,6,3))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
687 abline(v=c(maxvalue), col="red", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
688 abline(v=c(mzvalue), col="green2", lty=5)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
689 title(paste0("theor. m/z: ", inputcalibrants[count,1]), col.main="blue", outer=TRUE, line=0, adj=0.074)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
690 title(paste0("most abundant m/z: ", round(maxvalue, digits=4)), col.main="red", outer=TRUE, line=0, adj=0.49)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
691 title(paste0("closest m/z: ", round(mzvalue, digits=4)), col.main="green2", outer=TRUE, line=0, adj=0.93)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
692 count=count+1
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
693 }
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
694
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
695 ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range#########
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
696
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
697 par(mfrow = c(1, 1))
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
698
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
699 ### plot the ppm difference calculated above: theor. m/z value to highest m/z value:
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
700
7
b86a66dd1a16 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit dd64f41874a56c4e2619bf58ae3681d806cf9b3f
galaxyp
parents: 6
diff changeset
701 calibrant_names = as.character(inputcalibrants[,2])
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
702 diff_df = data.frame(differencevector, calibrant_names)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
703
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
704 if (sum(is.na(diff_df[,1])) == nrow(diff_df)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
705 print("plot 17: no peaks in the chosen region, repeat with higher ppm range")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
706 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
707
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
708 diff_plot=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
709 labs(title="Difference m/z with max. average intensity vs. theoretical calibrant m/z", x="calibrants", y = "Difference in ppm")+
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
710 geom_text(aes(label=differencevector), vjust=-0.3, size=3.5, col="blue")
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
711
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
712 print(diff_plot)}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
713
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
714 ######### 18) ppm difference input calibrant m/z and closest m/z ###########
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
715
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
716 ### plot the ppm difference calculated above theor. m/z value to closest m/z value:
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
717
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
718 differencevector2 = round(differencevector2, digits=2)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
719 calibrant_names = as.character(inputcalibrants[,2])
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
720 diff_df = data.frame(differencevector2, calibrant_names)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
721
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
722 diff_plot=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
723 labs(title="Difference closest measured m/z vs. theoretical calibrant m/z", x="calibrants", y = "Difference in ppm")+
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
724 geom_text(aes(label=differencevector2), vjust=-0.3, size=3.5, col="blue")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
725
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
726 print(diff_plot)
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
727
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
728 #################### 19) ppm difference over pixels #####################
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
729
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
730 mycolours = c("darkgrey", "darkblue", "blue", "green" , "red", "orange", "yellow", "magenta", "olivedrab1", "lightseagreen")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
731 count = 1
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
732 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata)))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
733 for (calibrant in inputcalibrantmasses){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
734 ### 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
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
735 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
736
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
737 if (nrow(filtered_data) > 0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
738 ### filtered for m/z range, now go through it pixel by pixel to find max peak in each spectrum
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
739 ppm_vector = numeric()
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
740 for (pixel_count in 1:ncol(filtered_data)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
741 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])]
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
742
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
743 mzdiff = mz_max - calibrant
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
744 ppmdiff = mzdiff/calibrant*1000000
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
745
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
746 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
747 if (max(spectra(filtered_data)[,pixel_count]) == 0){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
748 ppmdiff = NA}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
749 ppm_vector[pixel_count] = ppmdiff}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
750 }else{ppm_vector = rep(NA, ncol(msidata))}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
751
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
752 ppm_df = cbind(ppm_df, ppm_vector)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
753 count=count+1}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
754
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
755 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_df)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
756 print("plot 19: no peaks in the chosen region, repeat with higher ppm range")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
757 }else{
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
758
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
759 ### plot ppm differences over pixels (spectra index)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
760
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
761 par(mar=c(4.1, 4.1, 4.1, 7.5))
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
762 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. theoretical m/z\n(per spectrum)")
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
763
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
764 for (each_cal in 1:ncol(ppm_df)){
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
765 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
766 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
767 abline(v=abline_vector, lty = 3)}
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
768
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
769 }else{print("16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")}
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
770
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
771 dev.off()
6
5c63fe03ed9e planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
772
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
773 }else{
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
774 print("inputfile has no intensities > 0")
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
775 dev.off()
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
776 }
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
777
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
778 ]]></configfile>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
779 </configfiles>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
780 <inputs>
3
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
781 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
782 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
783 <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
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
784 <param name="calibrant_file" type="data" optional="true" format="tabular"
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
785 label="File with internal calibrants" help="first column: m/z, second column: name (optional), tabular file"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
786 <param name="peptide_file" type="data" optional="true" format="tabular" label="File with m/z of interest"
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
787 help="first column: m/z, second column: name (optional), tabular file"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
788 <param name="plusminus_dalton" value="0.25" type="float" label="M/z range for m/z heatmaps (x-y grid)" help="Will be added in both directions to input calibrants and peptide m/z"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
789 <param name="plusminus_ppm" value="50" type="float" label="Ppm range for accuracy and number of calibrants plots" help="Will be added in both directions to input calibrant m/z"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
790 <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10">
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
791 <param name="mass1" value="1111" type="float" label="M/z 1" help="First m/z"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
792 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
793 <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
f6aa0cff777c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
794 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
795 </repeat>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
796 </inputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
797 <outputs>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
798 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "$infile.display_name QC_report"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
799 </outputs>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
800 <tests>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
801 <test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
802 <param name="infile" value="" ftype="imzml">
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
803 <composite_data value="Example_Continuous.imzML" />
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
804 <composite_data value="Example_Continuous.ibd" />
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
805 </param>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
806 <param name="peptide_file" value="inputpeptides.txt"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
807 <param name="calibrant_file" value="inputcalibrantfile1.txt"/>
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
808 <param name="plusminus_dalton" value="0.25"/>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
809 <param name="plusminus_ppm" value="100"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
810 <param name="filename" value="Testfile_imzml"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
811 <repeat name="calibrantratio">
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
812 <param name="mass1" value="328.9"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
813 <param name="mass2" value="398.8"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
814 <param name="distance" value="0.25"/>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
815 <param name="filenameratioplot" value = "Ratio of mass1 (328.9) / mass2 (398.8)"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
816 </repeat>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
817 <output name="plots" file="QC_imzml.pdf" compare="sim_size" delta="20000"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
818 </test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
819 <test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
820 <param name="infile" value="" ftype="analyze75">
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
821 <composite_data value="Analyze75.hdr"/>
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
822 <composite_data value="Analyze75.img"/>
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
823 <composite_data value="Analyze75.t2m"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
824 </param>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
825 <param name="peptide_file" value="inputpeptides.txt"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
826 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
827 <param name="plusminus_dalton" value="0.5"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
828 <param name="filename" value="Testfile_analyze75"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
829 <output name="plots" file="QC_analyze75.pdf" compare="sim_size" delta="20000"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
830 </test>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
831 <test>
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
832 <param name="infile" value="123_combined.RData" ftype="rdata"/>
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
833 <param name="plusminus_dalton" value="0.2"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
834 <param name="filename" value="Testfile_rdata"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
835 <output name="plots" file="QC_rdata.pdf" compare="sim_size" delta="20000"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
836 </test>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
837 <test>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
838 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
839 <param name="peptide_file" value="inputpeptides.txt"/>
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
840 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
841 <param name="plusminus_dalton" value="0.1"/>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
842 <param name="filename" value="Testfile_rdata"/>
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
843 <output name="plots" file="QC_empty_spectra.pdf" compare="sim_size" delta="20000"/>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
844 </test>
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
845 </tests>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
846 <help>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
847 <![CDATA[
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
848 Cardinal is an R package that implements statistical & computational tools for analyzing mass spectrometry imaging datasets. `More information on Cardinal <http://cardinalmsi.org//>`_
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
849
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
850 This tool uses some Cardinal functions to create a quality control report with descriptive plots for mass spectrometry imaging data.
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
851
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
852 Input data: 3 types of input data can be used:
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
853
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
854 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <https://ms-imaging.org/wp/imzml/>`_
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
855 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
856 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
857
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
858 Options:
4
fef8bd551236 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
859
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
860 - 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
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
861 - m/z of interest are used to generate m/z heatmaps (x-y grid)
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
862 - optional fold change plot: draws a heatmap (x-y grid) for the fold change of two m/z (log2(intensity ratio))
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
863
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
864 Output:
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
865
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
866 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data
8
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
867
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
868 Tip:
52ef77866de8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 1c808d60243bb1eeda0cd26cb4b0a17ab05de2c0
galaxyp
parents: 7
diff changeset
869
9
963c7ec00141 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit a7be47698f53eb4f00961192327d93e8989276a7
galaxyp
parents: 8
diff changeset
870 - For additional m/z heatmaps use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool.
0
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
871
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
872 ]]>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
873 </help>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
874 <citations>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
875 <citation type="doi">10.1093/bioinformatics/btv146</citation>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
876 </citations>
845073d506a8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
877 </tool>
2
1ccbda92b76b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
878