Mercurial > repos > galaxyp > cardinal_quality_report

annotate quality_report.xml @ 0:5f18275c250a draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
author galaxyp
date Mon, 01 Oct 2018 01:07:13 -0400
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5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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1 <tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.0">
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2 <description>
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3 mass spectrometry imaging QC
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4 </description>
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5 <macros>
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6 <import>macros.xml</import>
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7 </macros>
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8 <expand macro="requirements">
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9 <requirement type="package" version="2.2.1">r-ggplot2</requirement>
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10 <requirement type="package" version="1.1_2">r-rcolorbrewer</requirement>
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11 <requirement type="package" version="2.2.1">r-gridextra</requirement>
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12 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
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13 <requirement type="package" version="0.5.0">r-scales</requirement>
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14 <requirement type="package" version="1.0.8"> r-pheatmap</requirement>
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15 </expand>
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16 <command detect_errors="exit_code">
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17 <![CDATA[
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18 @INPUT_LINKING@
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19 cat '${cardinal_qualitycontrol_script}' &&
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20 Rscript '${cardinal_qualitycontrol_script}'
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21 ]]>
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22 </command>
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23 <configfiles>
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24 <configfile name="cardinal_qualitycontrol_script"><![CDATA[
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25
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26 ################################# load libraries and read file #################
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27
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28 library(Cardinal)
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29 library(ggplot2)
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30 library(RColorBrewer)
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31 library(gridExtra)
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32 library(KernSmooth)
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33 library(scales)
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34 library(pheatmap)
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35
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36 @READING_MSIDATA@
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37
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38 ## remove duplicated coordinates
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39 print(paste0(sum(duplicated(coord(msidata))), " duplicated coordinates were removed"))
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40 msidata <- msidata[,!duplicated(coord(msidata))]
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41
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42 ## create full matrix to make processed imzML files compatible with segmentation and other steps
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43 iData(msidata) <- iData(msidata)[]
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45 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
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46
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47 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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48
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49 ## read and extract x,y,annotation information
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50 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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51 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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52 annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
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53 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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54
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55 ## merge with coordinate information of msidata
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56 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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57 colnames(msidata_coordinates)[3] = "pixel_index"
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58 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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59 merged_annotation[is.na(merged_annotation)] = "NA"
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60 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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61 msidata\$annotation = as.factor(merged_annotation[,4])
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62
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63 #end if
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64
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65 ###################### calculation of data properties ################################
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66 @DATA_PROPERTIES@
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67
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68 ## Median intensities
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69 medint = round(median(spectra(msidata)[], na.rm=TRUE), digits=2)
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70 ## Spectra multiplied with m/z (potential number of peaks)
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71 numpeaks = ncol(spectra(msidata)[])*nrow(spectra(msidata)[])
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72 ## Percentage of intensities > 0
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73 percpeaks = round(npeaks/numpeaks*100, digits=2)
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74 ## Number of empty TICs
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75 TICs = colSums(spectra(msidata)[], na.rm=TRUE)
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76 NumemptyTIC = sum(TICs == 0)
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77 ## Median und sd TIC
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78 medTIC = round(median(TICs), digits=1)
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79 sdTIC = round(sd(TICs), digits=0)
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80 ## Median and sd # peaks per spectrum
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81 medpeaks = round(median(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE), digits=0)
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82 sdpeaks = round(sd(colSums(spectra(msidata)[]>0, na.rm=TRUE), na.rm=TRUE), digits=0)
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83 print(cor(TICs,colSums(spectra(msidata)[]>0), method="pearson"))
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84 ## Processing informations
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85 centroidedinfo = centroided(msidata)
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86
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87 ############## Read and filter tabular file with m/z ###########################
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88
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89 ### reading calibrant file:
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90
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91 #if $calibrant_file:
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92
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93 calibrant_list = read.delim("$calibrant_file", header = $calibrant_header, na.strings=c("","NA"), stringsAsFactors = FALSE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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94 calibrant_list = calibrant_list[,c($mz_column, $name_column)]
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95
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96 ### calculate how many input calibrant m/z are valid:
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97
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98 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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99 number_calibrants_in = length(calibrant_list[,1])
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100 number_calibrants_valid = length(inputcalibrants[,1])
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101
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102 #else
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103
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104 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
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105 number_calibrants_in = 0
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106 number_calibrants_valid = 0
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107
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108 #end if
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109
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110 ## rename input dataframe and extract m/z
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111 colnames(inputcalibrants) = c("m/z", "name")
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112 inputcalibrantmasses = inputcalibrants[,1]
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113
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114
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115 ######################################## PDF #############################################
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116 ##########################################################################################
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117 ##########################################################################################
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118
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119 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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120 plot(0,type='n',axes=FALSE,ann=FALSE)
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121
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122 ## if no filename is given, name of file in Galaxy history is used
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123
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124 #if not $filename:
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125 #set $filename = $infile.display_name
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126 #end if
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127
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128 title(main=paste("$filename"))
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129
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130 ################# I) file properties in numbers ################################
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131 ################################################################################
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132 print("properties in numbers")
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133
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134 properties2 = c("Median of intensities",
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135 "Intensities > 0",
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136 "Number of empty spectra",
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137 "Median TIC ± sd",
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138 "Median # peaks per spectrum ± sd",
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139 "Centroided",
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140 paste0("calibrants (#valid/#input) in \n", "$calibrant_file.display_name"))
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141
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142 values2 = c(paste0(medint),
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143 paste0(percpeaks, " %"),
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144 paste0(NumemptyTIC),
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145 paste0(medTIC, " ± ", sdTIC),
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146 paste0(medpeaks, " ± ",sdpeaks),
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147 paste0(centroidedinfo),
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148 paste0(number_calibrants_valid, " / ", number_calibrants_in))
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149
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150 property_df2 = data.frame(properties2, values2)
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151 colnames(property_df2) = c("properties", "values")
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152
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153 property_df = rbind(property_df, property_df2)
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154
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155 grid.table(property_df, rows= NULL)
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156
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157
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158 ####################### II) x-y images #######################################
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159 ##############################################################################
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160 print("x-y images")
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161
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162 ## only do plots for file with intensity peaks
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163 if (npeaks > 0){
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164 ## function for density plots
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165 plot_colorByDensity = function(x1,x2,
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166 ylim=c(min(x2),max(x2)),
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167 xlim=c(min(x1),max(x1)),
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168 xlab="",ylab="",main=""){
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169 df = data.frame(x1,x2)
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170 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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171 df\$dens = col2rgb(x)[1,] + 1L
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172 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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173 df\$col = cols[df\$dens]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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174 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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175 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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176
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177
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178 ################### 0) overview for combined data ###########################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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179
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180 ### only for previously combined data, same plot as in combine QC pdf
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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181
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182 if (!is.null(levels(msidata\$annotation))){
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183
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184 number_combined = length(levels(msidata\$annotation))
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185
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186 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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187 colnames(position_df)[3] = "annotation"
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188
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189 combine_plot = ggplot(position_df, aes(x=x, y=y, fill=annotation))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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190 geom_tile() +
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191 coord_fixed()+
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192 ggtitle("Spatial orientation of pixel annotations")+
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193 theme_bw()+
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194 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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195 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
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196 theme(legend.position="bottom",legend.direction="vertical")+
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197 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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198
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199 print(combine_plot)
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200
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201 ## for each annotation group find last pixel, there dashed lines will be drawn in plots over spectra index
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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202 pixel_name_df = data.frame(pixels(msidata), msidata\$annotation)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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203 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
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204 last_pixel = aggregate(pixel_number~pixel_name, data = pixel_name_df, max)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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205 pixel_vector = last_pixel[,2]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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206 abline_vector = pixel_vector[1:number_combined-1]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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207 print(abline_vector)
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208 }
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209
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210 ################### 1) Pixel order image ###################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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211
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212 pixelnumber = 1:pixelcount
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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213 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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214 gg_title = "Pixel order"
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215
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216 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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217 geom_tile() + coord_fixed()+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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218 ggtitle(gg_title) + theme_bw()+
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219 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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220 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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221 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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222 space = "Lab", na.value = "black", name = "Pixel\nnumber"))
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223
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224 ################ 2) Number of calibrants per spectrum ######################
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225
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226 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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227 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
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228
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229 ## plot only possible when there is at least one valid calibrant
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230 if (length(inputcalibrantmasses) != 0){
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231
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232 ## calculate plusminus values in m/z for each calibrant
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233 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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234
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235 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
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236
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237 for (mass in 1:length(inputcalibrantmasses)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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238
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239 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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240
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241 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data)[],na.rm=TRUE) > 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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242
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243 ## intensity of all m/z > 0
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244 intensity_sum = colSums(spectra(filtered_data)[], na.rm=TRUE) > 0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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245
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246 }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data)[], na.rm=TRUE) > 0){
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247
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248 ## intensity of only m/z > 0
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249 intensity_sum = spectra(filtered_data)[] > 0
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250
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251 }else{
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252
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253 intensity_sum = rep(FALSE, ncol(filtered_data))}
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254
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255 ## for each pixel add sum of intensities > 0 in the given m/z range
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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256 pixelmatrix = rbind(pixelmatrix, intensity_sum)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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257 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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258
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259 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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260 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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261 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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262 mycolours = c("black","grey", "darkblue", "blue", "green" , "red", "yellow", "magenta", "olivedrab1", "lightseagreen")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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263
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264 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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265 geom_tile() + coord_fixed() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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266 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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267 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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268 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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269 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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270 scale_fill_manual(values = mycolours[1:length(countvector)],
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271 na.value = "black", name = "# calibrants"))
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272
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273 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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274
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275 ########################## 3) fold change image ###########################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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276
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277 #if $calibrantratio:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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278 #for $foldchanges in $calibrantratio:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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279 mass1 = $foldchanges.mass1
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280 mass2 = $foldchanges.mass2
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281 distance = $foldchanges.distance
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282
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283 ### if user did not write a label use input m/z as label
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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284 #if not str($foldchanges.filenameratioplot).strip():
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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285 #set $label = "Fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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286 #else:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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287 #set $label = $foldchanges.filenameratioplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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288 #end if
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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289
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290 ### filter msidata for given m/z range (for both input m/z)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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291 filtered_data1 = msidata[mz(msidata) >= mass1-distance & mz(msidata) <= mass1+distance,]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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292 filtered_data2 = msidata[mz(msidata) >= mass2-distance & mz(msidata) <= mass2+distance,]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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293
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294 ### find m/z in the two given ranges with the highest mean intensity
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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295 ### this two m/z will be used to calculate the fold change (red line in plot)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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296 maxmassrow1 = rowMeans(spectra(filtered_data1), na.rm=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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297 maxmass1 = mz(filtered_data1)[which.max(maxmassrow1)]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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298 maxmassrow2 = rowMeans(spectra(filtered_data2), na.rm=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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299 maxmass2 = mz(filtered_data2)[which.max(maxmassrow2)]
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300
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301 ### plot legend: chosen value in blue, distance in blue, max m/z in red
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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302 ### m/z range for each plot (fixed range of 5 Da)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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303 ### xlim does not work because it does not adjust for the max. intensities within the range
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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304 mzdown1 = features(msidata, mz = mass1-2)
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305 mzup1 = features(msidata, mz = mass1+3)
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306 mzdown2 = features(msidata, mz = mass2-2)
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307 mzup2 = features(msidata, mz = mass2+3)
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308
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309 ### plot for first m/z
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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310 par(mfrow=c(2,1), oma=c(0,0,2,0))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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311 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("Average spectrum ", mass1, " Da"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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312 abline(v=c(mass1-distance, mass1, mass1+distance), col="blue",lty=c(3,6,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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313 abline(v=maxmass1, col="red", lty=5)
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314
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315 ### plot for second m/z
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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316 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("Average spectrum ", mass2, " Da"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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317 abline(v=c(mass2-distance, mass2, mass2+distance), col="blue", lty=c(3,6,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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318 abline(v=maxmass2, col="red", lty=5)
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319 title("Control of fold change plot", outer=TRUE)
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320
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321 ### filter spectra for max m/z to have two vectors, which can be divided
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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322 ### plot spatial distribution of fold change
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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323 ### only possible when there are intensities > 0 in both given m/z ranges
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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324
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325 if (length(maxmass1)>0&length(maxmass2)>0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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326 mass1vector = spectra(msidata)[features(msidata, mz = maxmass1),]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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327 mass2vector = spectra(msidata)[features(msidata, mz = maxmass2),]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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328 foldchange= log2(mass1vector/mass2vector)
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329 fcmatrix = cbind(foldchange, coord(msidata)[,1:2])
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330
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331 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange), colour=colo)+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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332 geom_tile() + coord_fixed()+
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333 ggtitle("$label")+
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334 theme_bw()+
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335 theme(plot.title = element_text(hjust = 0.5))+
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336 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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337 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
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338 ,space = "Lab", na.value = "black", name ="FC"))
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339 }else{
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340 plot(0,type='n',axes=FALSE,ann=FALSE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
341 title(main=paste("At least one m/z range did not contain any intensity > 0,\n therefore no foldchange plot could be drawn"))}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
342
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
343 #end for
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
344 #end if
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
345
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
346 #################### 4) m/z heatmaps #######################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
347
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
348 par(mfrow=c(1,1), mar=c(5.1, 4.1, 4.1, 2.1), mgp=c(3, 1, 0), las=0)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
349 if (length(inputcalibrants[,1]) != 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
350 for (mass in 1:length(inputcalibrants[,1])){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
351
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
352
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
353 image(msidata, mz=inputcalibrants[,1][mass], plusminus=plusminusvalues[mass],
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
354 main= paste0(inputcalibrants[,2][mass], ": ", round(inputcalibrants[,1][mass], digits = 2)," (±",$plusminus_ppm, " ppm)"),
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
355 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
356 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
357 } else {print("4) The input peptide and calibrant m/z were not provided or outside the m/z range")}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
358
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
359 #################### 5) Number of peaks per pixel - image ##################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
360
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
361 ## here every intensity value > 0 counts as peak
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
362 peaksperpixel = colSums(spectra(msidata)[]> 0, na.rm=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
363 peakscoordarray=cbind(coord(msidata)[,1:2], peaksperpixel)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
364
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
365 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel), colour=colo)+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
366 geom_tile() + coord_fixed() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
367 ggtitle("Number of peaks per spectrum")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
368 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
369 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
370 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
371 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
372 ,space = "Lab", na.value = "black", name = "# peaks"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
373
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
374
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
375 ############################### 6) TIC image ###############################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
376
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
377 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
378 colo = colorRampPalette(
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379 c("blue", "cyan", "green", "yellow","red"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
380 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs), colour=colo)+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
381 geom_tile() + coord_fixed() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
382 ggtitle("Total Ion Chromatogram")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
383 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
384 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
385 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
386 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
387 ,space = "Lab", na.value = "black", name = "TIC"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
388
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
389
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
390 ############################### 7) Most abundant m/z image #################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
391
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
392 highestmz = apply(spectra(msidata)[],2,which.max)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
393 highestmz_matrix = cbind(coord(msidata)[,1:2],mz(msidata)[highestmz])
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
394 colnames(highestmz_matrix)[3] = "highestmzinDa"
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
395
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
396 print(ggplot(highestmz_matrix, aes(x=x, y=y, fill=highestmzinDa))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
397 geom_tile() + coord_fixed() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
398 ggtitle("Most abundant m/z in each spectrum")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
399 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
400 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
401 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"), space = "Lab", na.value = "black", name = "m/z",
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
402 limits=c(min(highestmz_matrix\$highestmzinDa), max(highestmz_matrix\$highestmzinDa)))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
403 theme(text=element_text(family="ArialMT", face="bold", size=12)))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
404
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
405
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
406 ########################## 8) optional pca image for two components #################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
407
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
408 #if $do_pca:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
409
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
410 pca = PCA(msidata, ncomp=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
411 par(mfrow = c(2,1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
412 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
413 image(pca, col=c("black", "white"), strip=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-0.2*minimumy))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
414
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
415 #end if
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
416
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
417 ################## III) properties over spectra index ######################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
418 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
419 print("properties over pixels")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
420 par(mfrow = c(2,1), mar=c(5,6,4,2))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
421
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
422 ########################## 9) number of peaks per spectrum #################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
423 ## 9a) scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
424
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
425 plot_colorByDensity(pixels(msidata), peaksperpixel, ylab = "", xlab = "", main="Number of peaks per spectrum")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
426 title(xlab="Spectra index", line=3)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
427 title(ylab="Number of peaks", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
428
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
429 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
430 abline(v=abline_vector, lty = 3)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
431
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432 ## 9b) histogram
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
434 hist(peaksperpixel, main="", las=1, xlab = "Number of peaks per spectrum", ylab="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
435 title(main="Number of peaks per spectrum", line=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
436 title(ylab="Frequency = # spectra", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
437 abline(v=median(peaksperpixel), col="blue")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
438
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
439 ## 9c) additional histogram to show contribution of annotation groups
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
440
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
441 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
442
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
443 df_9 = data.frame(peaksperpixel, msidata\$annotation)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
444 colnames(df_9) = c("Npeaks", "annotation")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
445
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
446 hist_9 = ggplot(df_9, aes(x=Npeaks, fill=annotation)) +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
447 geom_histogram()+ theme_bw()+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
448 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
450 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
451 theme(legend.position="bottom",legend.direction="vertical")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
452 labs(title="Number of peaks per spectrum and annotation group", x="Number of peaks per spectrum", y = "Frequency = # spectra") +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
454 geom_vline(xintercept = median(peaksperpixel), size = 1, colour = "black",linetype = "dashed")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
455 print(hist_9)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
456
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
457 ########################## 10) TIC per spectrum ###########################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
458
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
459 ## 10a)density scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
460 par(mfrow = c(2,1), mar=c(5,6,4,2))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
461
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 title(xlab="Spectra index", line=3)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
464 title(ylab = "Total ion chromatogram intensity", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
465 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
466 abline(v=abline_vector, lty = 3)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
467
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
468 ## 10b) histogram
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
469 hist(log(TICs), main="", las=1, xlab = "log(TIC per spectrum)", ylab="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
470 title(main= "TIC per spectrum", line=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 title(ylab="Frequency = # spectra", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
472 abline(v=median(log(TICs[TICs>0])), col="blue")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
473
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
474 ## 10c) additional histogram to show annotation contributions
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
475 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
476 df_10 = data.frame(log(TICs), msidata\$annotation)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
477 colnames(df_10) = c("TICs", "annotation")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
478
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
479 hist_10 = ggplot(df_10, aes(x=TICs, fill=annotation)) +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
480 geom_histogram()+ theme_bw()+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
481 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483 theme(legend.position="bottom",legend.direction="vertical")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
484 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
485 labs(title="TIC per spectrum and annotation group", x="log(TIC per spectrum)", y = "Frequency = # spectra") +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
486 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
487 geom_vline(xintercept = median(log(TICs[TICs>0])), size = 1, colour = "black",linetype = "dashed")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
488 print(hist_10)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
489
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
490 ################################## IV) properties over m/z ####################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
491 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
492 print("properties over m/z")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
493
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
494 ########################## 11) Histogram of m/z values #####################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
495
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 par(mfrow = c(1, 1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
497 hist(mz(msidata), xlab = "m/z", main="Histogram of m/z values")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
498
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 ########################## 12) Number of peaks per m/z #####################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
500
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
501 peakspermz = rowSums(spectra(msidata)[] > 0, na.rm=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
502 print(median(peakspermz/pixelcount*100))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
503
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
504 par(mfrow = c(2,1), mar=c(5,6,4,4.5))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
505 ## 12a) scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
506 plot_colorByDensity(mz(msidata),peakspermz, main= "Number of peaks per m/z", ylab ="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
507 title(xlab="m/z", line=2.5)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 title(ylab = "Number of peaks", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
509 axis(4, at=pretty(peakspermz),labels=as.character(round((pretty(peakspermz)/pixelcount*100), digits=1)), las=1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 mtext("Coverage of spectra [%]", 4, line=3, adj=1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
511
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
512 ## 12b) histogram
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 hist(peakspermz, main="", las=1, ylab="", xlab="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
514 title(ylab = "Frequency", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
515 title(main="Number of peaks per m/z", xlab = "Number of peaks per m/z", line=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
516 abline(v=median(peakspermz), col="blue")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
517
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
518 ########################## 13) Sum of intensities per m/z ##################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
519
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
520 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
521 mzTIC = rowSums(spectra(msidata)[], na.rm=TRUE) ## calculate intensity sum for each m/z
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
522
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523 par(mfrow = c(2,1), mar=c(5,6,4,2))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 ## 13a) scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
525 plot_colorByDensity(mz(msidata),mzTIC, main= "Sum of intensities per m/z", ylab ="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 title(xlab="m/z", line=2.5)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527 title(ylab="Intensity sum", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
528
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
529 ## 13b) histogram
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
530 hist(log(mzTIC), main="", xlab = "", las=1, ylab="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
531 title(main="Sum of intensities per m/z", line=2, ylab="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
532 title(xlab = "log (sum of intensities per m/z)")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
533 title(ylab = "Frequency", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
534 abline(v=median(log(mzTIC[mzTIC>0])), col="blue")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
535
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
536 ################################## V) intensity plots ########################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
537 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 print("intensity plots")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
539 ########################## 14) Intensity distribution ######################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
540
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 par(mfrow = c(2,1), mar=c(5,6,4,2))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
542
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543 ## 14a) Median intensity over spectra
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
544
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
545 medianint_spectra = apply(spectra(msidata), 2, median, na.rm=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
546 plot(medianint_spectra, main="Median intensity per spectrum",las=1, xlab="Spectra index", ylab="")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 title(ylab="Median spectrum intensity", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
548 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
549 abline(v=abline_vector, lty = 3)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
551 ## 14b) histogram:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552 hist(log2(spectra(msidata)[]), main="", xlab = "", ylab="", las=1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
553 title(main="Log2-transformed intensities", line=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
554 title(xlab="log2 intensities")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
555 title(ylab="Frequency", line=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
556 abline(v=median(log2(spectra(msidata)[(spectra(msidata)>0)]), na.rm=TRUE), col="blue")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
557
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
558
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 ## 14c) histogram to show contribution of annotation groups
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
560
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
562
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
563 df_13 = data.frame(matrix(,ncol=2, nrow=0))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
564 for (subsample in levels(msidata\$annotation)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565 log2_int_subsample = log2(spectra(msidata)[,msidata\$annotation==subsample])
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
566 df_subsample = data.frame(as.numeric(log2_int_subsample))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567 df_subsample\$annotation = subsample
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
568 df_13 = rbind(df_13, df_subsample)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 df_13\$annotation = as.factor(df_13\$annotation)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
570 colnames(df_13) = c("logint", "annotation")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
571
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572 hist_13 = ggplot(df_13, aes(x=logint, fill=annotation)) +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
573 geom_histogram()+ theme_bw()+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
574 theme(text=element_text(family="ArialMT", face="bold", size=12))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575 labs(title="Log2-transformed intensities per sample", x="log2 intensities", y = "Frequency") +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576 theme(plot.title = element_text(hjust = 0.5))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
577 theme(legend.position="bottom",legend.direction="vertical")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
578 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
579 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
580 geom_vline(xintercept = median(log2(spectra(msidata)[(spectra(msidata)>0)])), size = 1, colour = "black",linetype = "dashed")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
581 print(hist_13)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
582
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
583 ## 14d) boxplots to visualize in a different way the intensity distributions
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
584 par(mfrow = c(1,1), cex.axis=1.3, cex.lab=1.3, mar=c(13.1,4.1,5.1,2.1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
585
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
586 mean_matrix = matrix(,ncol=0, nrow = nrow(msidata))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
587 for (subsample in levels(msidata\$annotation)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
588 mean_mz_sample = rowMeans(spectra(msidata)[,msidata\$annotation==subsample],na.rm=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
589 mean_matrix = cbind(mean_matrix, mean_mz_sample)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
590
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
591 boxplot(log2(mean_matrix), ylab = "log2 mean intensity per m/z", main="Mean m/z intensities per annotation group", xaxt = "n")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
592 (axis(1, at = c(1:number_combined), labels=levels(msidata\$annotation), las=2))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
593
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
594 ## 14e) Heatmap of pearson correlation on mean intensities between annotation groups
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
596 corr_matrix = mean_matrix
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597 corr_matrix[corr_matrix == 0] <- NA
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
598 colnames(corr_matrix) = levels(msidata\$annotation)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
599 corr_matrix = cor(log2(corr_matrix), method= "pearson",use="complete.obs")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
600
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
601 heatmap.parameters <- list(corr_matrix,
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
602 show_rownames = T, show_colnames = T,
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
603 main = "Pearson correlation on mean intensities for each annotation group")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
604 do.call("pheatmap", heatmap.parameters)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
605 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
606
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
607 ################################## VI) Mass spectra and m/z accuracy ########################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
608 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
609 print("Mass spectra and m/z accuracy")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
610
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
611 ############################ 15) Mass spectra ##############################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
612
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
613 ## find three random pixel to plot their spectra in the following plots:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
614 pixel1 = sample(pixelnumber,1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
615 pixel2 = sample(pixelnumber,1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
616 pixel3 = sample(pixelnumber,1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
617
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
618 ## replace any NA with 0, otherwise plot function will not work at all
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
619 msidata_no_NA = msidata
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
620 spectra(msidata_no_NA)[is.na(spectra(msidata_no_NA)[])] = 0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
621
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
622 par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
623 plot(msidata_no_NA, pixel = 1:ncol(msidata_no_NA), main= "Average spectrum")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
624 plot(msidata_no_NA, pixel = pixel1, main=paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel1,1:2])))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
625 plot(msidata_no_NA, pixel = pixel2, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel2,1:2])))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
626 plot(msidata_no_NA, pixel = pixel3, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel3,1:2])))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
627
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
628 ################### 16) Zoomed in mass spectra for calibrants ##############
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
629
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
630 count = 1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
631 differencevector = numeric()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
632 differencevector2 = vector()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
633
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
634 if (length(inputcalibrantmasses) != 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
635
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
636 ### calculate plusminus values in m/z for each calibrant, this is used for all following plots
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
637 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses)) * inputcalibrantmasses
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
638
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
639 for (mass in 1:length(inputcalibrantmasses)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
640
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
641 ### define the plot window with xmin und xmax
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
642 minmasspixel = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
643 maxmasspixel = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+3)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
644
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
645 ### find m/z with the highest mean intensity in m/z range (red line in plot 16) and calculate ppm difference for plot 17
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
646 filtered_data = msidata_no_NA[mz(msidata_no_NA) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata_no_NA) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
647
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
648 if (nrow(filtered_data) > 0 & sum(spectra(filtered_data)) > 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
649 maxmassrow = rowMeans(spectra(filtered_data)) ## for each m/z average intensity is calculated
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
650 maxvalue = mz(filtered_data)[which.max(maxmassrow)] ### m/z with highest average intensity in m/z range
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
651 mzdifference = maxvalue - inputcalibrantmasses[mass] ### difference: theoretical value - closest m/z value
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
652 ppmdifference = mzdifference/inputcalibrantmasses[mass]*1000000 ### calculate ppm for accuracy measurement
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
653 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
654 ppmdifference = NA
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
655 maxvalue = NA}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
656 differencevector[mass] = round(ppmdifference, digits=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
657
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
658 ### find m/z closest to inputcalibrant and calculate ppm difference for plot 18
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
659 mznumber = features(msidata_no_NA, mz = inputcalibrantmasses[mass]) ### gives featurenumber which is closest to given m/z
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
660 mzvalue = mz(msidata_no_NA)[mznumber] ### gives closest m/z
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
661 mzdifference2 = mzvalue - inputcalibrantmasses[mass]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
662 ppmdifference2 = mzdifference2/inputcalibrantmasses[mass]*1000000
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
663 differencevector2[mass] = round(ppmdifference2, digits=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
664
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
665 par(mfrow = c(2, 2), oma=c(0,0,2,0))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
666 plot(msidata_no_NA[minmasspixel:maxmasspixel,], pixel = 1:length(pixelnumber), main= "Average spectrum")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
667 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
668 abline(v=c(maxvalue), col="red", lty=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
669 abline(v=c(mzvalue), col="green2", lty=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
670 plot(msidata_no_NA[minmasspixel:maxmasspixel,], pixel = pixel1, main=paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel1,1:2])))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
671 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
672 abline(v=c(maxvalue), col="red", lty=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
673 abline(v=c(mzvalue), col="green2", lty=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
674 plot(msidata_no_NA[minmasspixel:maxmasspixel,], pixel = pixel2, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel2,1:2])))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
675 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
676 abline(v=c(maxvalue), col="red", lty=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
677 abline(v=c(mzvalue), col="green2", lty=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
678 plot(msidata_no_NA[minmasspixel:maxmasspixel,], pixel = pixel3, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel3,1:2])))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
679 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="blue", lty=c(3,5,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
680 abline(v=c(maxvalue), col="red", lty=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
681 abline(v=c(mzvalue), col="green2", lty=4)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
682 title(paste0("theor. m/z: ", round(inputcalibrants[count,1], digits=4)), col.main="blue", outer=TRUE, line=0, adj=0.074)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
683 title(paste0("most abundant m/z: ", round(maxvalue, digits=4)), col.main="red", outer=TRUE, line=0, adj=0.49)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
684 title(paste0("closest m/z: ", round(mzvalue, digits=4)), col.main="green2", outer=TRUE, line=0, adj=0.93)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
685
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
686 ### 16b) one large extra plot with different colours for different pixel annotation groups
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
687
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
688 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
689 if (number_combined < 10){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
690 key_zoomed = TRUE
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
691 }else{key_zoomed = FALSE}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
692 par(mfrow = c(1, 1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
693 plot(msidata_no_NA[minmasspixel:maxmasspixel,], pixel=1:ncol(msidata_no_NA),main="Average spectrum per annotation group",
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
694 pixel.groups=msidata\$annotation, key=key_zoomed, col=hue_pal()(number_combined),superpose=TRUE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
695 abline(v=c(inputcalibrantmasses[mass] -plusminusvalues[count], inputcalibrantmasses[mass] ,inputcalibrantmasses[mass] +plusminusvalues[count]), col="black", lty=c(3,1,3))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
696 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
697 count=count+1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
698 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
699
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
700 ######### 17) ppm difference input calibrant m/z and m/z with max intensity in given m/z range#########
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
701
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
702 par(mfrow = c(1,1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
703 ### plot the ppm difference calculated above: theor. m/z value to highest m/z value:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
704
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
705 calibrant_names = as.character(inputcalibrants[,2])
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
706 diff_df = data.frame(differencevector, calibrant_names)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
707
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
708 if (sum(is.na(diff_df[,1])) == nrow(diff_df)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
709 plot(0,type='n',axes=FALSE,ann=FALSE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
710 title(main=paste("plot 17: no peaks in the chosen region, repeat with higher ppm range"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
711 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
712
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
713 diff_plot1=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
714 labs(title="Average m/z error (max. average intensity vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
715 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
716 geom_text(aes(label=differencevector), vjust=-0.3, size=5.5, col="blue") +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
717 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
718
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
719 print(diff_plot1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
720 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
721
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
722 ######### 18) ppm difference input calibrant m/z and closest m/z ###########
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
723
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
724 ### plot the ppm difference calculated above theor. m/z value to closest m/z value:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
725
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
726 differencevector2 = round(differencevector2, digits=2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
727 calibrant_names = as.character(inputcalibrants[,2])
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
728 diff_df = data.frame(differencevector2, calibrant_names)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
729
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
730 diff_plot2=ggplot(data=diff_df, aes(x=calibrant_names, y=differencevector2)) + geom_bar(stat="identity", fill = "darkgray") + theme_minimal() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
731 labs(title="Average m/z error (closest measured m/z vs. theor. calibrant m/z)", x="calibrants", y = "Average m/z error in ppm")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
732 theme(plot.title = element_text(hjust = 0.5, size=14))+theme(text=element_text(family="ArialMT", face="bold", size=14))+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
733 geom_text(aes(label=differencevector2), vjust=-0.3, size=5.5, col="blue")+
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
734 theme(axis.text.x = element_text(angle = 90, hjust = 1, size=14))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
735
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
736 print(diff_plot2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
737
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
738 #################### 19) ppm difference over pixels #####################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
739
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
740 par(mfrow = c(1,1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
741 mycolours = c("darkgrey", "darkblue", "blue", "green" , "red", "orange", "yellow", "magenta", "olivedrab1", "lightseagreen")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
742 count = 1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
743 ppm_df = as.data.frame(matrix(,ncol=0, nrow = ncol(msidata)))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
744 for (calibrant in inputcalibrantmasses){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
745 ### find m/z with the highest mean intensity in m/z range, if no m/z in the range, ppm differences for this calibrant will be NA
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
746 filtered_data = msidata[mz(msidata) >= calibrant-plusminusvalues[count] & mz(msidata) <= calibrant+plusminusvalues[count],]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
747
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
748 if (nrow(filtered_data) > 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
749 ### filtered for m/z range, find max peak in each spectrum (pixel)(
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
750 ppm_vector = numeric()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
751 for (pixel_count in 1:ncol(filtered_data)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
752 mz_max = mz(filtered_data)[which.max(spectra(filtered_data)[,pixel_count])]
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
753
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
754 mzdiff = mz_max - calibrant
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
755 ppmdiff = mzdiff/calibrant*1000000
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
756
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
757 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
758 if (max(spectra(filtered_data)[,pixel_count]) == 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
759 ppmdiff = NA}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
760 ppm_vector[pixel_count] = ppmdiff}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
761
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
762 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
763 ppm_vector = rep(NA, ncol(msidata))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
764 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
765
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
766 ppm_df = cbind(ppm_df, ppm_vector)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
767 count=count+1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
768 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
769
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
770 if (sum(is.na(ppm_df)) == ncol(ppm_df)*nrow(ppm_df)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
771 plot(0,type='n',axes=FALSE,ann=FALSE)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
772 title(main=paste("plot 19: no peaks in the chosen region, repeat with higher ppm range"))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
773 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
774
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
775 ### plot ppm differences over pixels (spectra index)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
776 par(mar=c(4.1, 4.1, 4.1, 7.5))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
777
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
778 plot(0,0,type="n", ylim=c(min(ppm_df, na.rm=TRUE),max(ppm_df, na.rm=TRUE)), xlim = c(1,ncol(filtered_data)),xlab = "Spectra index", ylab = "m/z difference in ppm", main="Difference m/z with max. average intensity vs. theor. m/z\n(per spectrum)")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
779 for (each_cal in 1:ncol(ppm_df)){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
780 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
781 legend("topright", inset=c(-0.25,0), xpd = TRUE, bty="n", legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
782 if (!is.null(levels(msidata\$annotation))){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
783 abline(v=abline_vector, lty = 3)}}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
784
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
785 }else{print("plot 16+17+18+19) The inputcalibrant m/z were not provided or outside the m/z range")}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
786 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
787 print("inputfile has no intensities > 0")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
788 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
789 dev.off()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
790
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
791
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
792 ]]></configfile>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
793 </configfiles>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
794 <inputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
795 <expand macro="reading_msidata"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
796 <conditional name="tabular_annotation">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
797 <param name="load_annotation" type="select" label="Use pixel annotation from tabular file for QC plots">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
798 <option value="no_annotation" selected="True">pixels belong into one group only</option>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
799 <option value="yes_annotation">use pixel annotation from a tabular file</option>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
800 </param>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
801 <when value="yes_annotation">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
802 <expand macro="reading_pixel_annotations"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
803 </when>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
804 <when value="no_annotation"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
805 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
806 <expand macro="pdf_filename"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
807 <expand macro="reading_2_column_mz_tabular"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
808 <param name="plusminus_ppm" value="200" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
809 <param name="do_pca" type="boolean" label="PCA with 2 components"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
810 <repeat name="calibrantratio" title="Plot fold change of two m/z" min="0" max="10">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
811 <param name="mass1" value="1111" type="float" label="M/z 1" help="First m/z"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
812 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
813 <param name="distance" value="0.25" type="float" label="M/z range" help="Plusminus m/z window added to input m/z. In both m/z ranges the maximum intensity is used to calculate the fold change"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
814 <param name="filenameratioplot" type="text" optional="true" label="Title" help="Optional title for fold change plot.">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
815 <sanitizer invalid_char="">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
816 <valid initial="string.ascii_letters,string.digits">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
817 <add value="_" />
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
818 </valid>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
819 </sanitizer>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
820 </param>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
821 </repeat>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
822 <param name="pixel_output" type="boolean" label="Tabular output with spectra information"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
823 </inputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
824 <outputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
825 <data format="pdf" name="QC_report" from_work_dir="qualitycontrol.pdf" label = "${tool.name} on ${on_string}"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
826 </outputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
827 <tests>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
828 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
829 <expand macro="infile_imzml"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
830 <conditional name="processed_cond">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
831 <param name="processed_file" value="processed"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
832 <param name="accuracy" value="200"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
833 <param name="units" value="ppm"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
834 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
835 <conditional name="tabular_annotation">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
836 <param name="load_annotation" value="no_annotation"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
837 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
838 <param name="calibrant_file" value="inputcalibrantfile1.tabular" ftype="tabular"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
839 <param name="mz_column" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
840 <param name="name_column" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
841 <param name="plusminus_ppm" value="100"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
842 <param name="filename" value="Testfile_imzml"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
843 <param name="do_pca" value="True"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
844 <repeat name="calibrantratio">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
845 <param name="mass1" value="328.9"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
846 <param name="mass2" value="398.8"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
847 <param name="distance" value="0.25"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
848 <param name="filenameratioplot" value = "Ratio of mass1 (328.9) / mass2 (398.8)"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
849 </repeat>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
850 <output name="QC_report" file="QC_imzml.pdf" compare="sim_size"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
851 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
852
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
853 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
854 <expand macro="infile_analyze75"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
855 <conditional name="tabular_annotation">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
856 <param name="load_annotation" value="no_annotation"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
857 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
858 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
859 <param name="mz_column" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
860 <param name="name_column" value="2"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
861 <param name="filename" value="Testfile_analyze75"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
862 <param name="do_pca" value="True"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
863 <output name="QC_report" file="QC_analyze75.pdf" compare="sim_size"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
864 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
865
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
866 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
867 <param name="infile" value="3_files_combined.RData" ftype="rdata"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
868 <conditional name="tabular_annotation">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
869 <param name="load_annotation" value="yes_annotation"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
870 <param name="annotation_file" value="annotations_rdata.tabular"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
871 <param name="column_x" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
872 <param name="column_y" value="2"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
873 <param name="column_names" value="3"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
874 <param name="tabular_header" value="True"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
875 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
876 <param name="calibrant_file" value="inputcalibrantfile1.tabular" ftype="tabular"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
877 <param name="mz_column" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
878 <param name="name_column" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
879 <param name="plusminus_ppm" value="100"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
880 <param name="filename" value="Testfile_rdata"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
881 <param name="do_pca" value="True"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
882 <output name="QC_report" file="QC_rdata.pdf" compare="sim_size"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
883 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
884 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
885 <param name="infile" value="empty_spectra.rdata" ftype="rdata"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
886 <conditional name="tabular_annotation">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
887 <param name="load_annotation" value="no_annotation"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
888 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
889 <param name="calibrant_file" value="inputcalibrantfile2.txt"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
890 <param name="mz_column" value="1"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
891 <param name="name_column" value="2"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
892 <param name="filename" value="Testfile_rdata"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
893 <param name="do_pca" value="False"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
894 <output name="QC_report" file="QC_empty_spectra.pdf" compare="sim_size"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
895 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
896 </tests>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
897 <help>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
898 <![CDATA[
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
899 @CARDINAL_DESCRIPTION@
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
900
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
901 -----
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
902
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
903 This tool uses Cardinal to read files and create a quality control report with descriptive plots for mass spectrometry imaging data.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
904
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
905 @MSIDATA_INPUT_DESCRIPTION@
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
906 - Coordinates stored as decimals rather than integers will be rounded to obtain a regular pixel grid. This might lead to duplicated coordinates which will be automatically removed before the tools analysis starts.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
907 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
908
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
909 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
910
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
911 **Options**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
912
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
913 - m/z of interest (e.g. internal calibrants) and the ppm range are used for m/z heatmaps (x-y grid), heatmap of number of calibrants per spectrum (x-y grid), zoomed in mass spectra, m/z accuracy plots
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
914 - Optional fold change plot: draws a heatmap (x-y grid) for the fold change of two m/z (log2(intensity ratio))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
915 - All plots are described in more detail below
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
916
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
917 **Tip**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
918
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
919 - For additional m/z heatmaps use the MSI mz images tool and to plot more mass spectra use the MSI mass spectra tool.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
920 - To obtain the underlaying spectra and feature values used in this quality report, the imzML exporter tool can be used
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
921
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
922
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
923 **Output**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
924
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
925 - quality control report as pdf with key numbers and descriptive plots describing the mass spectrometry imaging data
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
926
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
927
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
928 ----------------------------------------------------------------------------------------------------------------------------------------------------
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
929
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
930 **Overview of the QC report plots**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
931
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
932 - (annot): this plots will only be drawn if pixel annotations are loaded via a tabular file
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
933 - (cal): this plots will only be drawn if a tabular file with at least one valid calibrant m/z is provided
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
934 - (FC): this plots will only be drawn if the optional fold change image is selected
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
935 - Vertical lines in histograms represent median values. In density scatter plots the colour changes from blue to green, yellow and red the more points are overlayed.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
936
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
937 - Overview of file properties: Numbers and ranges for m/z features and pixels are given. Median and range across all intensity values are provided. Intensities > 0 gives the percentage of m/z-pixel pairs with an intensity above zero. The number of empty spectra (TIC = 0), the median number of peaks (intensities > 0) per spectra as well as the median TIC (total ion chromatogram) are given. The processing status of the file is provided as well as the number of valid calibrants from the provided tabular file.> 0 (Intensities > 0).
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
938
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
939 **x-y images (pixel/spectra information)**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
940
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
941 - (annot) Spatial orientation of annotated pixel: All pixels of one annotation group have the same colour.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
942 - Pixel order: Shows the order of the pixels in the provided file. Depending on the instrument this can represent the acquisition order. If annotation file is provided pixels are ordered according to annotation groups.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
943 - (cal) Number of calibrants per pixel: In every spectrum the calibrant m/z window (calibrant m/z plusminus 'ppm range') is searched for peaks (intensity > 0). Calibrants are considered present in a spectrum when they have at least one peak in their m/z window.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
944 - (FC) Control of fold change plot: For both input m/z a zoomed in average spectrum is drawn with the input m/z as blue dashed line, the m/z range as blue dotted lines and the maximum intensity in the m/z window with a red line.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
945 - (FC) Fold change image: For each spectrum the intensities of the two optimal m/z features (red lines in control plots) are divided and log2 transformed to obtain the fold change, which is then plotted as a heatmap.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
946 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z. The intensities are averaged within the calibrant m/z window (ppm range).
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
947 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
948 - Total ion chromatogram: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
949 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
950 - PCA for two components: Result of a principal component analysis (PCA) for two components is given. The loading plot depicts the contribution of each m/z value and the x-y image represents the differences between the pixels.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
951
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
952 **Properties over spectra/pixels**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
953
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
954 - Number of peaks per spectrum: Scatter plot and histogram showing the number of intensities > 0 for each spectrum. If annotation tabular file is provided, the pixels are sorted according to annotation groups and the dotted lines in the scatter plot separate spectra of different annotation groups.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
955 - (annot) Number of peaks per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
956 - TIC per spectrum: Scatter plot and histogram showing the sum of all intensities per spectrum (TIC). Dotted lines in the scatter plot separate spectra of different annotation groups.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
957 - (annot) TIC per spectrum and annotation group: Same histogram as in plot before but with colours to show the contribution of each pixel annotation group.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
958
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
959 **Properties over m/z features**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
960
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
961 - Histogram of m/z values: Histogram of all m/z values (complete m/z axis)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
962 - Number of peaks per m/z: Scatter plot and histogram giving the number of intensities > 0 for each m/z.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
963 - Sum of intensities per m/z: Scatter plot and histogram of the sum of all intensities per m/z.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
964
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
965 **Intensity plots**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
966
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
967 - Median intensity per spectrum: Scatter plot in which each point represents the median intensity for one spectrum. Dotted lines in the scatter plot separate spectra of different annotation groups.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
968 - Log2-transformed intensities: Histogram of log2-transformed intensities.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
969 - (annot) log2-transformed intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
970 - (annot) Mean intensities per m/z and annotation group: For all pixels of an annotation group the mean intensity for each m/z is calculated and shown as boxplot.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
971 - (annot) Pearson correlation between annotation groups based on mean intensities and shown as heatmap.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
972
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
973 **Mass spectra and m/z accuracy**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
974
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
975 - Mass spectra over the full m/z range: First plot shows the average intensities over all spectra. The other three mass spectra are from random individual pixels (spectra).
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
976 - (cal) For each calibrant four zoomed in mass spectrum are drawn: The first shows the average intensities over all spectra and the other three are single mass spectra. The theoretical calibrant m/z (taken from the input file) is represented by the dashed blue line. The dotted blue lines show the given ppm range. The green line is the m/z value that is closest to the theoretical calibrant and the red line is the m/z with the highest average intensity in the m/z window.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
977 - (annot) Average spectrum per annotation group: For each calibrant a zoomed in mass spectrum is plotted this time with the average intensities for each annotation group separately.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
978 - (cal) Difference m/z with max. average intensity vs. theor. calibrant m/z: The difference in ppm between the m/z with the highest average intensity and the theoretical m/z are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the red line in the zoomed in mass spectra.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
979 - (cal) Difference closest measured m/z vs. theor. calibrant m/z: The difference in ppm between the closest m/z value and the theoretical m/z values are plotted for each calibrant. This corresponds to the difference between the dashed blue line and the green line in the zoomed in mass spectra.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
980 - (cal) Difference m/z with max. average intensity vs. theor. m/z (per spectrum): For each spectrum the ppm difference between the m/z with the highest average intensity and the theoretical m/z are plotted. The calibrants have different plotting colours. Dashed lines separate spectra of different annotation groups.
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
981
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
982
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
983 ]]>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
984 </help>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
985 <expand macro="citations"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
986 </tool>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
987