Mercurial > repos > galaxyp > msi_qualitycontrol

annotate msi_qualitycontrol.xml @ 4:f44e887bd5b7 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
author galaxyp
date Thu, 01 Mar 2018 08:24:22 -0500
parents 62cd51699137
children ae98f109ba68
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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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1 <tool id="mass_spectrometry_imaging_qc" name="MSI Qualitycontrol" version="1.7.0.3">
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2 <description>
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3 mass spectrometry imaging QC
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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>
0
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10 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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>
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29 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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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f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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40 msidata = readMSIData('infile.imzML')
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41 #elif $infile.ext == 'analyze75'
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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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42 msidata = readMSIData('infile.hdr')
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43
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44 #else
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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 {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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89 normalizationinfo=processinginfo@normalization
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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90 }
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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91 ## smoothing
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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92 if (length(processinginfo@smoothing) == 0) {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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93 smoothinginfo='FALSE'
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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94 } else {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
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95 smoothinginfo=processinginfo@smoothing
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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96 }
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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97 ## baseline
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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98 if (length(processinginfo@baselineReduction) == 0) {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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99 baselinereductioninfo='FALSE'
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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100 } else {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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101 baselinereductioninfo=processinginfo@baselineReduction
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102 }
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103 ## peak picking
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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104 if (length(processinginfo@peakPicking) == 0) {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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105 peakpickinginfo='FALSE'
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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106 } else {
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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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:
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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111
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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112 #if $peptide_file:
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113
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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114 input_list = read.delim("$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 {
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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117 input_list = cbind(input_list, input_list)
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118 }
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119
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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120 ### calculate how many input peptide masses are valid:
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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121 inputpeptides = input_list[input_list[,1]>minmz & input_list[,1]<maxmz,]
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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122 number_peptides_in = length(input_list[,1])
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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123 number_peptides_valid = length(inputpeptides)
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124
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125 #else
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126 inputpeptides = data.frame(0,0)
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127 number_peptides_in = 0
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128 number_peptides_valid = 0
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129 #end if
2
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130
4
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131 colnames(inputpeptides) = c("mz", "name")
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132
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133 #if $calibrant_file:
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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134 ### Read tabular file with calibrant masses:
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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135 calibrant_list = read.delim("$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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136 if (ncol(calibrant_list) == 1)
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137 {
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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138 calibrant_list = cbind(calibrant_list, calibrant_list)
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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139 }
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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140 ### calculate how many input calibrant masses are valid:
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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141 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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142 number_calibrants_in = length(calibrant_list[,1])
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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143 number_calibrants_valid = length(inputcalibrants)
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144 #else
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145 inputcalibrants = data.frame(0,0)
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146 number_calibrants_in = 0
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147 number_calibrants_valid = 0
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148 #end if
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149
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150 colnames(inputcalibrants) = c("mz", "name")
0
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151
2
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152 ### bind inputcalibrants and inputpeptides together, to make heatmap on both lists
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153
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154 inputs_all = rbind(inputcalibrants[,1:2], inputpeptides[,1:2])
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155 inputmasses = inputs_all[,1]
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156 inputnames = inputs_all[,2]
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157
0
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158
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159 properties = c("Number of mz features",
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160 "Range of mz values [Da]",
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161 "Number of pixels",
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162 "Range of x coordinates",
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163 "Range of y coordinates",
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164 "Range of intensities",
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165 "Median of intensities",
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166 "Intensities > 0",
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167 "Number of zero TICs",
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168 "Preprocessing",
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169 "Normalization",
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170 "Smoothing",
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171 "Baseline reduction",
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172 "Peak picking",
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173 "Centroided",
4
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174 paste0("# peptides in ", "$peptide_file.display_name"),
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175 paste0("# calibrants in ", "$calibrant_file.display_name"))
0
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176
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177 values = c(paste0(maxfeatures),
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178 paste0(minmz, " - ", maxmz),
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179 paste0(pixelcount),
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180 paste0(minimumx, " - ", maximumx),
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181 paste0(minimumy, " - ", maximumy),
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182 paste0(minint, " - ", maxint),
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183 paste0(medint),
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184 paste0(percpeaks, " %"),
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185 paste0(NumemptyTIC),
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186 paste0(" "),
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187 paste0(normalizationinfo),
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188 paste0(smoothinginfo),
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189 paste0(baselinereductioninfo),
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190 paste0(peakpickinginfo),
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191 paste0(centroidedinfo),
4
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192 paste0(number_peptides_valid, " / " , number_peptides_in),
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193 paste0(number_calibrants_valid, " / ", number_calibrants_in))
0
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194
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195
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196 property_df = data.frame(properties, values)
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197
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198 ######################################## PDF #############################################
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199 ##########################################################################################
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200 ##########################################################################################
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201
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202 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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203 plot(0,type='n',axes=FALSE,ann=FALSE)
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204 #if not $filename:
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205 #set $filename = $infile.display_name
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206 #end if
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207 title(main=paste("Quality control of MSI data\n\n", "Filename:", "$filename"))
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208
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209 ############################# I) numbers ####################################
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210 #############################################################################
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211 grid.table(property_df, rows= NULL)
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212
2
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213 if (npeaks > 0)
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214 {
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215 ############################# II) ion images #################################
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216 ##############################################################################
0
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217
2
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218 ## function without xaxt for plots with automatic x axis
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219 plot_colorByDensity = function(x1,x2,
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220 ylim=c(min(x2),max(x2)),
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221 xlim=c(min(x1),max(x1)),
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222 xlab="",ylab="",main=""){
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223
4
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224 df = data.frame(x1,x2)
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225 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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226 df\$dens = col2rgb(x)[1,] + 1L
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227 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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228 df\$col = cols[df\$dens]
2
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229 plot(x2~x1, data=df[order(df\$dens),],
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230 ylim=ylim,xlim=xlim,pch=20,col=col,
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231 cex=1,xlab=xlab,ylab=ylab,las=1,
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232 main=main)
0
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233 }
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234
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235
2
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236 ############################################################################
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237
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238 ## 1) Acquisition image
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239
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240 pixelnumber = 1:pixelcount
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241 pixelxyarray=cbind(coord(msidata),pixelnumber)
0
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242
2
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243 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))
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244 + geom_tile() + coord_fixed()
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245 + ggtitle("1) Order of Acquisition")
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246 +theme_bw()
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247 + 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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248 space = "Lab", na.value = "black", name = "Acq"))
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249
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250 ## 2) Number of calibrants per spectrum
0
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251
2
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252 pixelmatrix = matrix(ncol=ncol(msidata), nrow=0)
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253 inputcalibrantmasses = inputcalibrants[,1]
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254
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255 if (length(inputcalibrantmasses) != 0)
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256 { for (calibrantnr in 1:length(inputcalibrantmasses))
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257 {
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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258 calibrantmz = inputcalibrantmasses[calibrantnr]
4
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259 calibrantfeaturemin = features(msidata, mz=calibrantmz-$plusminus_dalton)
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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260 calibrantfeaturemax = features(msidata, mz=calibrantmz+$plusminus_dalton)
0
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261
2
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262 if (calibrantfeaturemin == calibrantfeaturemax)
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263 {
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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264
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265 calibrantintensity = spectra(msidata)[calibrantfeaturemin,]
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266
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267 }else{
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268
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269 calibrantintensity = colSums(spectra(msidata)[calibrantfeaturemin:calibrantfeaturemax,] )
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270
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271 }
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272 pixelmatrix = rbind(pixelmatrix, calibrantintensity)
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273 }
0
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274
2
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275 countvector= as.factor(colSums(pixelmatrix>0))
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276 countdf= cbind(coord(msidata), countvector)
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277 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
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278
2
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279 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))
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280 + geom_tile() + coord_fixed()
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281 + ggtitle("2) Number of calibrants per pixel")
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282 + theme_bw()
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283 + theme(text=element_text(family="ArialMT", face="bold", size=12))
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284 + scale_fill_manual(values = mycolours[1:length(countvector)],
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285 na.value = "black", name = "# calibrants"))
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286 }else{print("2) The inputcalibrant masses were not provided or outside the mass range")}
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287
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288
2
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289 ############# new 2b) image of foldchanges (log2 intensity ratios) between two masses in the same spectrum
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290
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291 #if $calibrantratio:
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292 #for $foldchanges in $calibrantratio:
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293 mass1 = $foldchanges.mass1
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294 mass2 = $foldchanges.mass2
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295 distance = $foldchanges.distance
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296
3
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297 #if not str($foldchanges.filenameratioplot).strip():
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298 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
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299 #else:
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300 #set $label = $foldchanges.filenameratioplot
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301 #end if
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302
2
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303 ### find rows which contain masses:
0
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304
2
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305 mzrowdown1 = features(msidata, mz = mass1-distance)
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306 mzrowup1 = features(msidata, mz = mass1+distance)
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307 mzrowdown2 = features(msidata, mz = mass2-distance)
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308 mzrowup2 = features(msidata, mz = mass2+distance)
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309
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310 ### lower and upperlimit for the plot
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311 mzdown1 = features(msidata, mz = mass1-2)
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312 mzup1 = features(msidata, mz = mass1+3)
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313 mzdown2 = features(msidata, mz = mass2-2)
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314 mzup2 = features(msidata, mz = mass2+3)
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315
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316 ### find mass in the given range with the highest intensity (will be plotted in red)
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317
2
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318 if (mzrowdown1 == mzrowup1)
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319 {
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320 maxmass1 = mz(msidata)[ mzrowdown1]
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321 }else{ ### for all masses in the massrange calculate mean intensity over all pixels and take mass which has highest mean
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322 maxmassrow1 = rowMeans(spectra(msidata)[mzrowdown1:mzrowup1,])
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323 maxmass1 = mz(msidata)[mzrowdown1:mzrowup1][which.max(maxmassrow1)]
2
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324 }
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325 if (mzrowdown2 == mzrowup2)
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326 {
4
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327 maxmass2 = mz(msidata)[mzrowup2]
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328 }else{
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329 maxmassrow2 = rowMeans(spectra(msidata)[mzrowdown2:mzrowup2,])
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330 maxmass2 = mz(msidata)[mzrowdown2:mzrowup2][which.max(maxmassrow2)]
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331 }
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332
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333 ### 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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334 par(mfrow=c(2,1), oma=c(0,0,2,0))
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335 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("average spectrum ", mass1, " Da"))
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336 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,5,3))
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337 abline(v=maxmass1, col="red", lty=5)
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338
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339 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("average spectrum ", mass2, " Da"))
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340 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,5,3))
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341 abline(v=maxmass2, col="red", lty=5)
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342 title("Control of fold change plot", outer=TRUE)
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343
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344 ### filter spectra for maxmass to have two vectors, which can be divided
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345
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346 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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347 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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348 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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349
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
350 ratiomatrix = cbind(foldchange, coord(msidata))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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351
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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352 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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353 + geom_tile() + coord_fixed()
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
galaxyp
parents: 2
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354 + 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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355 + 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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356 + 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
357 + 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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358 ,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
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diff changeset
359 #end for
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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360 #end if
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
361
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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362 ## 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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363
3
62cd51699137 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit 9f8984da558d0a307fed3ff3af9313829d2e5baa
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364 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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365 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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366 { 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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367 {
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
368 image(msidata, mz=inputmasses[mass], plusminus=$plusminus_dalton,
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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369 main= paste0("3", LETTERS[mass], ") ", inputnames[mass], " (", round(inputmasses[mass], digits = 2)," ± ", $plusminus_dalton, " Da)"),
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
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diff changeset
370 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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parents: 1
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371 }
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
372 } else {print("3) The inputpeptide masses were outside the mass range")}
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
373
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
374 ## 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
galaxyp
parents: 1
diff changeset
375
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
376 peaksperpixel = colSums(spectra(msidata)[]> 0)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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377 peakscoordarray=cbind(coord(msidata), peaksperpixel)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
378
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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379 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
380 + geom_tile() + coord_fixed()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
381 + ggtitle("4) Number of peaks per pixel")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
382 + 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
383 + 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
384 + 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
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385 ,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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diff changeset
386
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
387 ## 5) TIC image
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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388 TICcoordarray=cbind(coord(msidata), 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
389 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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390 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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391 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
galaxyp
parents: 1
diff changeset
392 + geom_tile() + coord_fixed()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
393 + ggtitle("5) Total Ion Chromatogram")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
394 + 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
395 + 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
396 + 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
397 ,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
398
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
399 ## 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
400
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
401 highestmz = apply(spectra(msidata)[],2,which.max)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
402 highestmz_matrix = cbind(coord(msidata),mz(msidata)[highestmz])
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
403 colnames(highestmz_matrix)[3] = "highestmzinDa"
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
404
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
405 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
406 + geom_tile() + coord_fixed()
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
407 + ggtitle("6) Most abundant m/z in each pixel")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
408 + 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
409 + 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
410 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
411 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
412 + 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
413
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
414 ## which mz are highest
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
415 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
416 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
417
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
418 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
419 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
420
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
421 ## 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
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diff changeset
422 pca = PCA(msidata, ncomp=2)
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
423 par(mfrow = c(2,1))
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 plot(pca, col=c("black", "darkgrey"), main="7) PCA for two components")
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
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diff changeset
425 image(pca, col=c("black", "white"),ylim=c(maximumy+2, 0))
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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426
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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427
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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428 ############################# 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
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429 ##############################################################################
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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430
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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431 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
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432
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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433 ## 8a) number of peaks per spectrum - scatterplot
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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434 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="8a) Number of peaks per spectrum")
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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435 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
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436 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
437
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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438 ## 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
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439 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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440 title(main="8b) Number of peaks per spectrum", line=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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441 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
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442 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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443
4
f44e887bd5b7 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit edbf2a6cb50fb04d0db56a7557a64e3bb7a0806a
galaxyp
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444 ## 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
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diff changeset
445 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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446 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
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447 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="9a) TIC per pixel")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
448 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
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449 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
450
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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451 ## 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
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452 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
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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453 title(main= "9b) TIC per spectrum", line=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(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
455 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
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
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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458 ## 10) intensity of chosen peptides over acquisition (pixel index)
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
459
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 if (length(inputcalibrants[,1]) != 0)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
461 {
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
462 par(mfrow = c(3, 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
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diff changeset
463 intensityvector = vector()
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
464 for (mzvalue in 1:length(inputcalibrants[,1]))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
465 {
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
466 mznumber = features(msidata, mz = inputcalibrants[,1][mzvalue])
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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467 intensityvector = spectra(msidata)[][mznumber,]
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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468 plot(intensityvector, main=inputnames[mzvalue], xlab="Spectra index \n (= Acquisition time)")
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 }
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
470 title("10) intensity of calibrants over acquisition", outer=TRUE)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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471 }else{print("10) The inputcalibrant masses were outside the mass range")}
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
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472
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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473 ################################## IV) changes over mz ############################
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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474 ###################################################################################
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
475
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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476 ## 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
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diff changeset
477 ## 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
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478 peakspermz = rowSums(spectra(msidata)[] > 0 )
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
479
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
480 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
481 ## 11a) Number of peaks per mz - scatterplot
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
482 plot_colorByDensity(mz(msidata),peakspermz, main= "11a) Number of peaks for each mz", ylab ="")
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
483 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
484 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
485 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
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486 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
487
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
488 # make plot smaller to fit axis and labels, add second y axis with %
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
489 ## 11b) Number of peaks 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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diff changeset
490 hist(peakspermz, main="", las=1, ylab="")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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491 title(ylab = "Frequency", line=4)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
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diff changeset
492 title(main="11b) Number of peaks per mz", xlab = "Number of peaks per mz", line=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
493 abline(v=median(peakspermz), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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diff changeset
494
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
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495
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
496 ## 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
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diff changeset
497
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
498 ## 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
499 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
galaxyp
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diff changeset
500
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
501 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
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502 # 12a) sum of intensities per mz - scatterplot
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
503 plot_colorByDensity(mz(msidata),mzTIC, main= "12a) Sum of all peak intensities for each mz", ylab ="")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
504 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
505 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
506 # 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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507 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
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diff changeset
508 title(main="12b) Sum of intensities per mz", line=2, ylab="")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
509 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
510 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
511 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
512
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
513 ################################## V) general plots ############################
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
514 ###################################################################################
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
515
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
516 ## 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
517
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
518 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
519
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
520 ## 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
521 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
522 title(main="13a) Log2-transformed intensities", line=2)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
523 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
524 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
525 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
526
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
527 ## 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
528 medianint_spectra = apply(spectra(msidata), 2, median)
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
529 plot(medianint_spectra, main="13b) Median intensity per spectrum",las=1, xlab="Spectra index \n (= Acquisition time)", ylab="")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
530 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
531
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
532 ## 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
533
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
534 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
535 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
536 plot(msidata, pixel =round(length(pixelnumber)/2, digits=0), main="Spectrum in middle of acquisition")
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
537 plot(msidata, pixel = highestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[highestmz_pixel,])))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
538 plot(msidata, pixel = secondhighestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[secondhighestmz_pixel,])))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
539
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
540 ## 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
541 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
542 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
543 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
544 {
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
545
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
546 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
547 {
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
548 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
549 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
550 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
551 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
552 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
553 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
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 plot(msidata[minmasspixel:maxmasspixel,], pixel = highestmz_pixel,main= paste0("Spectrum at ", rownames(coord(msidata)[highestmz_pixel,])))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
556 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
557 plot(msidata[minmasspixel:maxmasspixel,], pixel = secondhighestmz_pixel, main= paste0("Spectrum at ", rownames(coord(msidata)[secondhighestmz_pixel,])))
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
558 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
559 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
560 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
561 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
562
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
563 }else{print("15) The inputcalibrant masses were 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
564
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
565 dev.off()
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
566 }else{
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
567 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
568 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
569 }
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
570
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
571 ]]></configfile>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
572 </configfiles>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
573 <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
574 <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
575 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
576 <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
577 <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
578 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
579 <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
580 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
581 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
582 <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
583 <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
584 <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
585 <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
586 <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
587 <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
588 </repeat>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
589 </inputs>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
590 <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
591 <data format="pdf" name="plots" from_work_dir="qualitycontrol.pdf" label = "${tool.name} on $infile.display_name"/>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
592 </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
593
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
594 <tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
595 <test>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
596 <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
597 <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
598 <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
599 </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
600 <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
601 <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
602 <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
603 <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
604 <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
605 <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
606 <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
607 <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
608 <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
609 </repeat>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
610 <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
611 </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
612
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
613 <test>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
614 <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
615 <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
616 <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
617 <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
618 </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
619 <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
620 <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
621 <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
622 <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
623 <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
624 </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
625
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
626 <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
627 <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
628 <param name="peptide_file" value="inputpeptides.csv" 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
629 <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
630 <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
631 <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
632 <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
633 </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
634 <test>
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
635 <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
636 <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
637 <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
638 <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
639 <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
640 <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
641 </test>
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
642 </tests>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
643 <help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
644 <![CDATA[
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 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
galaxyp
parents: 3
diff changeset
646 For additional beautiful heatmap images use the MSI ion images tool and to plot more mass spectra use the MSI massspectra tool.
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
647
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
648 Input data: 3 types of input data can be used:
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
649
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
650 - 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
galaxyp
parents:
diff changeset
651 - Analyze7.5 (upload hdr, img and t2m file via the "composite" function)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
652 - Cardinal "MSImageSet" data (with variable name "msidata", saved as .RData)
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
653
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
0
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
655
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
656 ]]>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
657 </help>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
658 <citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
659 <citation type="doi">10.1093/bioinformatics/btv146</citation>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
660 </citations>
348d4134ba6a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit fa798afa023eea1cb183c14d0242721b2c696c21
galaxyp
parents:
diff changeset
661 </tool>
2
4c81a6bffcf0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/msi_qualitycontrol commit a8eebad4ad469908f64c25e1e2c705eb637e3cae
galaxyp
parents: 1
diff changeset
662