Mercurial > repos > galaxyp > msi_qualitycontrol

annotate msi_qualitycontrol.xml @ 6:c54e7284ff31 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
author galaxyp
date Mon, 23 Apr 2018 17:17:30 -0400
parents ae98f109ba68
children ae9d7703ff27
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6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.5">
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2 <description>
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3 mass spectrometry imaging QC
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="1.7.0">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[
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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14 #if $infile.ext == 'imzml'
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15 cp '${infile.extra_files_path}/imzml' infile.imzML &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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16 cp '${infile.extra_files_path}/ibd' infile.ibd &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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17 #elif $infile.ext == 'analyze75'
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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18 cp '${infile.extra_files_path}/hdr' infile.hdr &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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19 cp '${infile.extra_files_path}/img' infile.img &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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20 cp '${infile.extra_files_path}/t2m' infile.t2m &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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21 #else
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22 ln -s '$infile' infile.RData &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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23 #end if
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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24 cat '${cardinal_qualitycontrol_script}' &&
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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25 Rscript '${cardinal_qualitycontrol_script}'
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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26 ]]>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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27 </command>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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28 <configfiles>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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29 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
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30
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31 library(Cardinal)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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32 library(ggplot2)
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33 library(RColorBrewer)
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34 library(gridExtra)
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35 library(KernSmooth)
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36
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37 ## Read MALDI Imaging dataset
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38
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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39 #if $infile.ext == 'imzml'
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40 msidata = readMSIData('infile.imzML')
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41 #elif $infile.ext == 'analyze75'
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42 msidata = readMSIData('infile.hdr')
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43
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44 #else
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45 load('infile.RData')
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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46 #end if
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47
2
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48
0
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49
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50 ###################################### file properties in numbers ######################
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51
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52 ## Number of features (mz)
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53 maxfeatures = length(features(msidata))
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54 ## Range mz
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55 minmz = round(min(mz(msidata)), digits=2)
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56 maxmz = round(max(mz(msidata)), digits=2)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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57 ## Number of spectra (pixels)
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58 pixelcount = length(pixels(msidata))
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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59 ## Range x coordinates
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60 minimumx = min(coord(msidata)[,1])
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61 maximumx = max(coord(msidata)[,1])
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62 ## Range y coordinates
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63 minimumy = min(coord(msidata)[,2])
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64 maximumy = max(coord(msidata)[,2])
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65 ## Range of intensities
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66 minint = round(min(spectra(msidata)[]), digits=2)
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67 maxint = round(max(spectra(msidata)[]), digits=2)
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68 medint = round(median(spectra(msidata)[]), digits=2)
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69 ## Number of intensities > 0
0
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70 npeaks= sum(spectra(msidata)[]>0)
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71 ## Spectra multiplied with mz (potential number of peaks)
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72 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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73 ## Percentage of intensities > 0
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74 percpeaks = round(npeaks/numpeaks*100, digits=2)
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75 ## Number of empty TICs
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76 TICs = colSums(spectra(msidata)[])
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77 NumemptyTIC = sum(TICs == 0)
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78
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79 ## Processing informations
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80 processinginfo = processingData(msidata)
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81 centroidedinfo = processinginfo@centroided # TRUE or FALSE
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82
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83 ## if TRUE write processinginfo if no write FALSE
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84
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85 ## normalization
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86 if (length(processinginfo@normalization) == 0) {
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87 normalizationinfo='FALSE'
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88 } else {
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89 normalizationinfo=processinginfo@normalization
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90 }
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91 ## smoothing
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92 if (length(processinginfo@smoothing) == 0) {
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93 smoothinginfo='FALSE'
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94 } else {
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95 smoothinginfo=processinginfo@smoothing
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96 }
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97 ## baseline
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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98 if (length(processinginfo@baselineReduction) == 0) {
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99 baselinereductioninfo='FALSE'
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100 } else {
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101 baselinereductioninfo=processinginfo@baselineReduction
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102 }
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103 ## peak picking
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104 if (length(processinginfo@peakPicking) == 0) {
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105 peakpickinginfo='FALSE'
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106 } else {
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107 peakpickinginfo=processinginfo@peakPicking
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108 }
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109
4
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110 ### Read tabular file with peptide masses for plots and heatmap images:
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111
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112 #if $peptide_file:
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113
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114 input_list = read.delim("$peptide_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
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115 if (ncol(input_list) == 1)
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116 {
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117 input_list = cbind(input_list, input_list)
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118 }
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119
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120 ### calculate how many input peptide masses are valid:
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121 inputpeptides = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
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122 number_peptides_in = length(input_list[,1])
5
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123 number_peptides_valid = length(inputpeptides[,1])
4
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124
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125 #else
5
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126 ###inputpeptides = data.frame(0,0)
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127 inputpeptides = as.data.frame(matrix(, nrow = 0, ncol = 2))
4
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128 number_peptides_in = 0
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129 number_peptides_valid = 0
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130 #end if
2
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131
4
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132 colnames(inputpeptides) = c("mz", "name")
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133
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134 #if $calibrant_file:
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135 ### Read tabular file with calibrant masses:
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136 calibrant_list = read.delim("$calibrant_file", header = FALSE, na.strings=c("","NA"), stringsAsFactors = FALSE)
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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137 if (ncol(calibrant_list) == 1)
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138 {
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139 calibrant_list = cbind(calibrant_list, calibrant_list)
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140 }
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141 ### calculate how many input calibrant masses are valid:
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142 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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143 number_calibrants_in = length(calibrant_list[,1])
5
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144 number_calibrants_valid = length(inputcalibrants[,1])
4
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145 #else
5
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146 ###inputcalibrants = data.frame(0,0)
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147
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148 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
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149
4
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150 number_calibrants_in = 0
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151 number_calibrants_valid = 0
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152 #end if
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153
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154 colnames(inputcalibrants) = c("mz", "name")
0
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155
2
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156 ### bind inputcalibrants and inputpeptides together, to make heatmap on both lists
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157
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158 inputs_all = rbind(inputcalibrants[,1:2], inputpeptides[,1:2])
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159 inputmasses = inputs_all[,1]
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160 inputnames = inputs_all[,2]
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161
0
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162
5
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163
0
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164 properties = c("Number of mz features",
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165 "Range of mz values [Da]",
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166 "Number of pixels",
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167 "Range of x coordinates",
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168 "Range of y coordinates",
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169 "Range of intensities",
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170 "Median of intensities",
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171 "Intensities > 0",
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172 "Number of zero TICs",
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173 "Preprocessing",
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174 "Normalization",
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175 "Smoothing",
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176 "Baseline reduction",
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177 "Peak picking",
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178 "Centroided",
5
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179 paste0("# peptides in \n", "$peptide_file.display_name"),
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180 paste0("# calibrants in \n", "$calibrant_file.display_name"))
0
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181
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182 values = c(paste0(maxfeatures),
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183 paste0(minmz, " - ", maxmz),
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184 paste0(pixelcount),
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185 paste0(minimumx, " - ", maximumx),
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186 paste0(minimumy, " - ", maximumy),
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187 paste0(minint, " - ", maxint),
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188 paste0(medint),
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189 paste0(percpeaks, " %"),
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190 paste0(NumemptyTIC),
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191 paste0(" "),
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192 paste0(normalizationinfo),
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193 paste0(smoothinginfo),
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194 paste0(baselinereductioninfo),
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195 paste0(peakpickinginfo),
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196 paste0(centroidedinfo),
4
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197 paste0(number_peptides_valid, " / " , number_peptides_in),
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198 paste0(number_calibrants_valid, " / ", number_calibrants_in))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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199
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200
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201 property_df = data.frame(properties, values)
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202
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203 ######################################## PDF #############################################
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204 ##########################################################################################
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205 ##########################################################################################
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206
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207 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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208 plot(0,type='n',axes=FALSE,ann=FALSE)
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209 #if not $filename:
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210 #set $filename = $infile.display_name
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211 #end if
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212 title(main=paste("Quality control of MSI data\n\n", "Filename:", "$filename"))
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213
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214 ############################# I) numbers ####################################
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215 #############################################################################
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216 grid.table(property_df, rows= NULL)
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217
2
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218 if (npeaks > 0)
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219 {
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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220 ############################# II) ion images #################################
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221 ##############################################################################
0
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222
2
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223 ## function without xaxt for plots with automatic x axis
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224 plot_colorByDensity = function(x1,x2,
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225 ylim=c(min(x2),max(x2)),
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226 xlim=c(min(x1),max(x1)),
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227 xlab="",ylab="",main=""){
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228
4
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229 df = data.frame(x1,x2)
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230 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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231 df\$dens = col2rgb(x)[1,] + 1L
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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232 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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233 df\$col = cols[df\$dens]
2
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234 plot(x2~x1, data=df[order(df\$dens),],
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235 ylim=ylim,xlim=xlim,pch=20,col=col,
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236 cex=1,xlab=xlab,ylab=ylab,las=1,
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237 main=main)
0
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238 }
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239
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240
2
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241 ############################################################################
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242
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diff changeset
243 ## 1) Acquisition image
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244
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245 pixelnumber = 1:pixelcount
6
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diff changeset
246 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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247
2
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248 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))
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249 + geom_tile() + coord_fixed()
6
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diff changeset
250 + ggtitle("Order of Acquisition")
2
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galaxyp
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diff changeset
251 +theme_bw()
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252 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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253 space = "Lab", na.value = "black", name = "Acq"))
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254
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diff changeset
255 ## 2) Number of calibrants per spectrum
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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256
2
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257 pixelmatrix = matrix(ncol=ncol(msidata), nrow=0)
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diff changeset
258 inputcalibrantmasses = inputcalibrants[,1]
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259
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260 if (length(inputcalibrantmasses) != 0)
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261 { for (calibrantnr in 1:length(inputcalibrantmasses))
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galaxyp
parents: 1
diff changeset
262 {
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
263 calibrantmz = inputcalibrantmasses[calibrantnr]
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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264 calibrantfeaturemin = features(msidata, mz=calibrantmz-$plusminus_dalton)
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265 calibrantfeaturemax = features(msidata, mz=calibrantmz+$plusminus_dalton)
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266
2
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267 if (calibrantfeaturemin == calibrantfeaturemax)
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268 {
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269
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270 calibrantintensity = spectra(msidata)[calibrantfeaturemin,]
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271
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272 }else{
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273
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274 calibrantintensity = colSums(spectra(msidata)[calibrantfeaturemin:calibrantfeaturemax,] )
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275
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276 }
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277 pixelmatrix = rbind(pixelmatrix, calibrantintensity)
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278 }
0
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279
2
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280 countvector= as.factor(colSums(pixelmatrix>0))
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281 countdf= cbind(coord(msidata)[,1:2], countvector)
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282 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
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283
2
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284 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))
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285 + geom_tile() + coord_fixed()
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286 + ggtitle("Number of calibrants per pixel")
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287 + theme_bw()
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288 + theme(text=element_text(family="ArialMT", face="bold", size=12))
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289 + scale_fill_manual(values = mycolours[1:length(countvector)],
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290 na.value = "black", name = "# calibrants"))
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291 }else{print("2) The inputcalibrant masses were not provided or outside the mass range")}
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292
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293
2
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294 ############# new 2b) image of foldchanges (log2 intensity ratios) between two masses in the same spectrum
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295
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296 #if $calibrantratio:
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297 #for $foldchanges in $calibrantratio:
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298 mass1 = $foldchanges.mass1
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299 mass2 = $foldchanges.mass2
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300 distance = $foldchanges.distance
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301
3
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302 #if not str($foldchanges.filenameratioplot).strip():
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303 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
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304 #else:
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305 #set $label = $foldchanges.filenameratioplot
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306 #end if
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307
2
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308 ### find rows which contain masses:
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309
2
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310 mzrowdown1 = features(msidata, mz = mass1-distance)
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311 mzrowup1 = features(msidata, mz = mass1+distance)
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312 mzrowdown2 = features(msidata, mz = mass2-distance)
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313 mzrowup2 = features(msidata, mz = mass2+distance)
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314
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315 ### lower and upperlimit for the plot
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316 mzdown1 = features(msidata, mz = mass1-2)
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317 mzup1 = features(msidata, mz = mass1+3)
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318 mzdown2 = features(msidata, mz = mass2-2)
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319 mzup2 = features(msidata, mz = mass2+3)
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320
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321 ### find mass in the given range with the highest intensity (will be plotted in red)
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322
2
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323 if (mzrowdown1 == mzrowup1)
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324 {
4
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325 maxmass1 = mz(msidata)[ mzrowdown1]
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326 }else{ ### for all masses in the massrange calculate mean intensity over all pixels and take mass which has highest mean
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327 maxmassrow1 = rowMeans(spectra(msidata)[mzrowdown1:mzrowup1,])
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328 maxmass1 = mz(msidata)[mzrowdown1:mzrowup1][which.max(maxmassrow1)]
2
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329 }
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330 if (mzrowdown2 == mzrowup2)
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331 {
4
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332 maxmass2 = mz(msidata)[mzrowup2]
2
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333 }else{
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334 maxmassrow2 = rowMeans(spectra(msidata)[mzrowdown2:mzrowup2,])
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335 maxmass2 = mz(msidata)[mzrowdown2:mzrowup2][which.max(maxmassrow2)]
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336 }
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337
4
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338 ### plot the part which was chosen, with chosen value in blue, distance in blue, maxmass in red, xlim fixed to 5 Da window
2
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339 par(mfrow=c(2,1), oma=c(0,0,2,0))
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340 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
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341 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,5,3))
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342 abline(v=maxmass1, col="red", lty=5)
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343
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344 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
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345 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,5,3))
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346 abline(v=maxmass2, col="red", lty=5)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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347 title("Control of fold change plot", outer=TRUE)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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348
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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349 ### filter spectra for maxmass to have two vectors, which can be divided
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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350
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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351 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),]
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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352 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),]
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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353 foldchange = log2(mass1vector/mass2vector)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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354
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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355 ratiomatrix = cbind(foldchange, coord(msidata)[,1:2])
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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356
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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357 print(ggplot(ratiomatrix, aes(x=x, y=y, fill=foldchange), colour=colo)
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
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358 + geom_tile() + coord_fixed()
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
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359 + ggtitle("$label")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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360 + theme_bw()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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361 + theme(text=element_text(family="ArialMT", face="bold", size=12))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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362 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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363 ,space = "Lab", na.value = "black", name ="FC"))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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364 #end for
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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365 #end if
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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366
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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367 ## 3) Calibrant images:
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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368
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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369 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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370 if (length(inputmasses) != 0)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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371 { for (mass in 1:length(inputmasses))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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372 {
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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diff changeset
373 image(msidata, mz=inputmasses[mass], plusminus=$plusminus_dalton,
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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374 main= paste0(inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"),
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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375 contrast.enhance = "histogram", ylim=c(maximumy+2, 0))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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376 }
5
ae98f109ba68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
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377 } else {print("3) The inputpeptide masses were not provided or outside the mass range")}
ae98f109ba68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
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diff changeset
378
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
379
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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380 ## 4) Number of peaks per pixel - image
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
381
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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382 peaksperpixel = colSums(spectra(msidata)[]> 0)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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383 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
384
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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385 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
386 + geom_tile() + coord_fixed()
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
387 + ggtitle("Number of peaks per pixel")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
388 + theme_bw()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
389 + theme(text=element_text(family="ArialMT", face="bold", size=12))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
390 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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391 ,space = "Lab", na.value = "black", name = "# peaks"))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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392
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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parents: 1
diff changeset
393 ## 5) TIC image
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
394 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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diff changeset
395 colo = colorRampPalette(
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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396 c("blue", "cyan", "green", "yellow","red"))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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397 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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parents: 1
diff changeset
398 + geom_tile() + coord_fixed()
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
399 + ggtitle("Total Ion Chromatogram")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
400 + theme_bw()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
401 + theme(text=element_text(family="ArialMT", face="bold", size=12))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
402 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
403 ,space = "Lab", na.value = "black", name = "TIC"))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
404
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
405 ## 6) Most abundant mass image
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
406
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
407 highestmz = apply(spectra(msidata)[],2,which.max)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
408 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz])
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
409 colnames(highestmz_matrix)[3] = "highestmzinDa"
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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diff changeset
410
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
411 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
412 + geom_tile() + coord_fixed()
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
413 + ggtitle("Most abundant m/z in each pixel")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
414 + theme_bw()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
415 + scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z",
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
416 labels = as.character(pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)]),
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
417 breaks = pretty(highestmz_matrix\$highestmzinDa)[c(1,3,5,7)], limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
418 + theme(text=element_text(family="ArialMT", face="bold", size=12)))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
419
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
420 ## which mz are highest
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
421 highestmz_peptides = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[1])
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
422 highestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == highestmz_peptides)[1]
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
423
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
424 secondhighestmz = names(sort(table(round(highestmz_matrix\$highestmzinDa, digits=0)), decreasing=TRUE)[2])
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
425 secondhighestmz_pixel = which(round(highestmz_matrix\$highestmzinDa, digits=0) == secondhighestmz)[1]
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
426
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
427 ## 7) pca image for two components
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
428 pca = PCA(msidata, ncomp=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
429 par(mfrow = c(2,1))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
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430 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
5
ae98f109ba68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 4
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431 image(pca, col=c("black", "white"),ylim=c(maximumy+2, 0), strip=FALSE)
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
432
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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433
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
434 ############################# III) properties over acquisition (spectra index)##########
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
435 ##############################################################################
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
436
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
437 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
438
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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439 ## 8a) number of peaks per spectrum - scatterplot
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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440 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
441 title(xlab="Spectra index \n (= Acquisition time)", line=3)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
442 title(ylab="Number of peaks", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
443
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
444 ## 8b) number of peaks per spectrum - histogram
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
445 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
446 title(main="Number of peaks per spectrum", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
447 title(ylab="Frequency = # spectra", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
448 abline(v=median(peaksperpixel), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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449
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
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450 ## 9a) TIC per spectrum - density scatterplot
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
451 zero=0
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
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452 par(mfrow = c(2,1), mar=c(5,6,4,2))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
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453 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
454 title(xlab="Spectra index \n (= Acquisition time)", line=3)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
455 title(ylab = "Total ion chromatogram intensity", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
456
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
457 ## 9b) TIC per spectrum - histogram
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
458 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
459 title(main= "TIC per spectrum", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
460 title(ylab="Frequency = # spectra", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
461 abline(v=median(log(TICs[TICs>0])), col="blue")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
462
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
463
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
464 ################################## IV) changes over mz ############################
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
465 ###################################################################################
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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466
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
467 ## 11) Number of peaks per mz
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
468 ## Number of peaks per mz - number across all pixel
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
469 peakspermz = rowSums(spectra(msidata)[] > 0 )
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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diff changeset
470
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
471 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
472 ## Number of peaks per mz - scatterplot
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
473 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per mz", ylab ="")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
474 title(xlab="mz in Dalton", line=2.5)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
475 title(ylab = "Number of peaks", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
476 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
477 mtext("Coverage of spectra [%]", 4, line=3, adj=1)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
478
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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479 # make plot smaller to fit axis and labels, add second y axis with %
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
480 ## Number of peaks per mz - histogram
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
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diff changeset
481 hist(peakspermz, main="", las=1, ylab="", xlab="")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
482 title(ylab = "Frequency", line=4)
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c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
483 title(main="Number of peaks per mz", xlab = "Number of peaks per mz", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
484 abline(v=median(peakspermz), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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diff changeset
485
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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diff changeset
486
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
487 ## 12) Sum of intensities per mz
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
488
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
489 ## Sum of all intensities for each mz (like TIC, but for mz instead of pixel)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
490 mzTIC = rowSums(spectra(msidata)[]) # calculate intensity sum for each mz
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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diff changeset
491
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
492 par(mfrow = c(2,1), mar=c(5,6,4,2))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
493 # 12a) sum of intensities per mz - scatterplot
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
494 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per mz", ylab ="")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
495 title(xlab="mz in Dalton", line=2.5)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
496 title(ylab="Intensity sum", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
497 # 12b) sum of intensities per mz - histogram
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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498 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
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diff changeset
499 title(main="Sum of intensities per mz", line=2, ylab="")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
500 title(xlab = "log (sum of intensities per mz)")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
501 title(ylab = "Frequency", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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502 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
503
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
504 ################################## V) general plots ############################
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
505 ###################################################################################
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
506
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
507 ## 13) Intensity distribution
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
508
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
509 par(mfrow = c(2,1), mar=c(5,6,4,2))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
510
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
511 ## 13a) Intensity histogram:
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
512 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
513 title(main="Log2-transformed intensities", line=2)
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
514 title(xlab="log2 intensities")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
515 title(ylab="Frequency", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
516 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)])), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
517
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
518 ## 13b) Median intensity over spectra
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
519 medianint_spectra = apply(spectra(msidata), 2, median)
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
520 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index \n (= Acquisition time)", ylab="")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
521 title(ylab="Median spectrum intensity", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
522
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
523 ## 13c) Histogram on mz values
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
524 par(mfrow = c(1, 1))
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
525 hist(mz(msidata), xlab = "mz in Dalton", main="Histogram of mz values")
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
526
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
527
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
528 ## 14) Mass spectra
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
529
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
530 par(mfrow = c(2, 2))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
531 plot(msidata, pixel = 1:length(pixelnumber), main= "Average spectrum")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
532 plot(msidata, pixel =round(length(pixelnumber)/2, digits=0), main="Spectrum in middle of acquisition")
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
533 plot(msidata, pixel = highestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[highestmz_pixel,1:2])))
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
534 plot(msidata, pixel = secondhighestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[secondhighestmz_pixel,1:2])))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
535
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
536 ## 15) Zoomed in mass spectra for calibrants
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
537 plusminusvalue = $plusminus_dalton
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
538 x = 1
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
539 if (length(inputcalibrantmasses) != 0)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
540 {
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
541
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
542 for (calibrant in inputcalibrantmasses)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
543 {
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
544 minmasspixel = features(msidata, mz=calibrant-1)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
545 maxmasspixel = features(msidata, mz=calibrant+3)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
546 par(mfrow = c(2, 2), oma=c(0,0,2,0))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
547 plot(msidata[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "average spectrum")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
548 abline(v=c(calibrant-plusminusvalue, calibrant,calibrant+plusminusvalue), col="blue", lty=c(3,5,3))
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
549 plot(msidata[minmasspixel:maxmasspixel,], pixel =round(length(pixelnumber)/2, digits=0), main="pixel in middle of acquisition")
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
550 abline(v=c(calibrant-plusminusvalue, calibrant,calibrant+plusminusvalue), col="blue", lty=c(3,5,3))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
551 plot(msidata[minmasspixel:maxmasspixel,], pixel = highestmz_pixel,main= paste0("Spectrum at ", rownames(coord(msidata)[highestmz_pixel,1:2])))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
552 abline(v=c(calibrant-plusminusvalue, calibrant,calibrant+plusminusvalue), col="blue", lty=c(3,5,3))
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
553 plot(msidata[minmasspixel:maxmasspixel,], pixel = secondhighestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[secondhighestmz_pixel,1:2])))
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
554 abline(v=c(calibrant-plusminusvalue, calibrant,calibrant+plusminusvalue), col="blue", lty=c(3,5,3))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
555 title(paste0(inputcalibrants[x,1]), outer=TRUE)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
556 x=x+1
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
557 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
558
5
ae98f109ba68 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit ed7d3e6f1a09c78c8f71cc1bdc1a20249767f646
galaxyp
parents: 4
diff changeset
559 }else{print("15) The inputcalibrant masses were not provided or outside the mass range")}
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
560
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
561 ## 16) ppm accuracy measured vs. theoretical calibrant mass
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
562
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
563 if (length(inputcalibrantmasses) != 0)
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
564 {
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
565 par(mfrow = c(1, 1))
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
566
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
567 differencevector = vector()
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
568
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
569 for (mass in 1:length(inputcalibrantmasses))
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
570 {mznumber = features(msidata, mz = inputcalibrantmasses[mass]) ### this gives the featurenumber which is closest to given mz
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
571 mzvalue = mz(msidata)[mznumber] ### gives the mz in Da which is closest to the given mz (using the featurenumber)
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
572 mzdifference = inputcalibrantmasses[mass] - mzvalue ### difference in Da: theoretical value - closest mz value
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
573 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
574 differencevector[mass] = ppmdifference }
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
575 differencevector = round(differencevector, digits=2)
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
576
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
577 ### plot the ppm difference theor. mz value to closest mz value:
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
578
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
579 calibrant_names = as.character(calibrant_list[,2])
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
580 diff_df = data.frame(differencevector, calibrant_names)
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
581 diff_plot<-ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_col() + theme_minimal() +
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
582 labs(title="Theoretical calibrant mz vs. closest measured mz", x="calibrants", y = "Difference in ppm")+
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
583 geom_text(aes(label=differencevector), vjust=-0.3, size=3.5, col="blue")
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
584
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
585 print(diff_plot)
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
586
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
587 }else{print("16) The inputcalibrant masses were not provided or outside the mass range")}
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
588
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
589
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
590 dev.off()
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
591
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
592 }else{
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
593 print("inputfile has no intensities > 0")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
594 dev.off()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
595 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
596
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
597 ]]></configfile>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
598 </configfiles>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
599 <inputs>
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
600 <param name="infile" type="data" format="imzml,rdata,analyze75" label="Inputfile as imzML, Analyze7.5 or Cardinal MSImageSet saved as RData"
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
601 help="Upload composite datatype imzml (ibd+imzML) or analyze75 (hdr+img+t2m) or regular upload .RData (Cardinal MSImageSet)"/>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
602 <param name="filename" type="text" value="" optional="true" label="Title" help="will appear in the quality report. If nothing given it will take the dataset name."/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
603 <param name="peptide_file" type="data" optional="true" format="tabular" label="Text file with peptidemasses and names"
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
604 help="first column peptide m/z, second column peptide name, tab separated file"/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
605 <param name="calibrant_file" type="data" optional="true" format="tabular"
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
606 label="Internal calibrants"
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
607 help="Used for plot number of calibrant per spectrum and for zoomed in mass spectra"/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
608 <param name="plusminus_dalton" value="0.25" type="text" label="Mass range" help="plusminus mass window in Dalton"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
609 <repeat name="calibrantratio" title="Plot fold change of two masses for each spectrum" min="0" max="10">
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
610 <param name="mass1" value="1111" type="float" label="Mass 1" help="First mass in Dalton"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
611 <param name="mass2" value="2222" type="float" label="Mass 2" help="Second mass in Dalton"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
612 <param name="distance" value="0.25" type="float" label="Distance in Dalton" help="Distance in Da used to find peak maximum from input masses in both directions"/>
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
diff changeset
613 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot."/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
614 </repeat>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
615 </inputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
616 <outputs>
6
c54e7284ff31 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msi_qualitycontrol commit 06c2b45d8644b1d7fc01622a5c59dcbf8886d0f1
galaxyp
parents: 5
diff changeset
617 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "${tool.name} ${on_string}"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
618 </outputs>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
619
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
620 <tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
621 <test>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
622 <param name="infile" value="" ftype="imzml">
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
623 <composite_data value="Example_Continuous.imzML" />
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
624 <composite_data value="Example_Continuous.ibd" />
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
625 </param>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
626 <param name="peptide_file" value="inputpeptides.csv" ftype="csv"/>
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
627 <param name="calibrant_file" ftype="txt" value="inputcalibrantfile1.txt"/>
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
628 <param name="plusminus_dalton" value="0.25"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
629 <param name="filename" value="Testfile_imzml"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
630 <repeat name="calibrantratio">
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
631 <param name="mass1" value="111"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
632 <param name="mass2" value="222"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
633 <param name="distance" value="0.25"/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
634 <param name="filenameratioplot" value = "Ratio of mass1 (111) / mass2 (222)"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
635 </repeat>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
636 <output name="plots" file="Testfile_qualitycontrol_imzml.pdf" compare="sim_size" delta="20000"/>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
637 </test>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
638
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
639 <test>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
640 <param name="infile" value="" ftype="analyze75">
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
641 <composite_data value="Analyze75.hdr"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
642 <composite_data value="Analyze75.img"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
643 <composite_data value="Analyze75.t2m"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
644 </param>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
645 <param name="peptide_file" value="inputpeptides.txt" ftype="txt"/>
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
646 <param name="calibrant_file" ftype="txt" value="inputcalibrantfile2.txt"/>
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
647 <param name="plusminus_dalton" value="0.5"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
648 <param name="filename" value="Testfile_analyze75"/>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
649 <output name="plots" file="Testfile_qualitycontrol_analyze75.pdf" compare="sim_size" delta="20000"/>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
650 </test>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
651
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
652 <test>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
653 <param name="infile" value="preprocessing_results1.RData" ftype="rdata"/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
654 <param name="plusminus_dalton" value="0.1"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
655 <param name="filename" value="Testfile_rdata"/>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
656 <output name="plots" file="Testfile_qualitycontrol_rdata.pdf" compare="sim_size" delta="20000"/>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
657 </test>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
658 <test>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
659 <param name="infile" value="LM8_file16.rdata" ftype="rdata"/>
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
660 <param name="peptide_file" value="inputpeptides.txt" ftype="txt"/>
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
661 <param name="calibrant_file" ftype="txt" value="inputcalibrantfile2.txt"/>
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
parents: 3
diff changeset
662 <param name="plusminus_dalton" value="0.1"/>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
663 <param name="filename" value="Testfile_rdata"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
664 <output name="plots" file="LM8_file16output.pdf" compare="sim_size" delta="20000"/>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
665 </test>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
666 </tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
667 <help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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668 <![CDATA[
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f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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669 Quality control for maldi imaging mass spectrometry data. The output of this tool contains key values and plots of the imaging data as pdf.
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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670 For additional beautiful heatmap images use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool.
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348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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671
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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672 Input data: 3 types of input data can be used:
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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673
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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674 - imzml file (upload imzml and ibd file via the "composite" function) `Introduction to the imzml format <http://ms-imaging.org/wp/introduction/>`_
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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675 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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676 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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677
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f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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678
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348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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679
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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680 ]]>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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681 </help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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682 <citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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683 <citation type="doi">10.1093/bioinformatics/btv146</citation>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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684 </citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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685 </tool>
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4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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686