Mercurial > repos > galaxyp > cardinal_quality_report

annotate quality_report.xml @ 5:f0d1f3e97303 draft

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"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
author galaxyp
date Fri, 06 Sep 2019 03:40:23 -0400
parents 3b7a35d50ebf
children bb9500286fe4
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f0d1f3e97303 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
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1 <tool id="cardinal_quality_report" name="MSI Qualitycontrol" version="@VERSION@.4">
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2 <description>
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3 mass spectrometry imaging QC
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4 </description>
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5 <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="1.1_2">r-rcolorbrewer</requirement>
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10 <requirement type="package" version="2.3">r-gridextra</requirement>
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11 <requirement type="package" version="3.0">r-ggplot2</requirement>
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12 <requirement type="package" version="2.23_15">r-kernsmooth</requirement>
1
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13 <requirement type="package" version="1.0.0">r-scales</requirement>
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14 <requirement type="package" version="1.0.10"> 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
1
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36
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37 @READING_MSIDATA_INRAM@
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38
0
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39 ## remove duplicated coordinates
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40 msidata <- msidata[,!duplicated(coord(msidata))]
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41
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42 ## optional annotation from tabular file to obtain pixel groups (otherwise all pixels are considered to be one sample)
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43
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44 #if str($tabular_annotation.load_annotation) == 'yes_annotation':
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45
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46 ## read and extract x,y,annotation information
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47 input_tabular = read.delim("$tabular_annotation.annotation_file", header = $tabular_annotation.tabular_header, stringsAsFactors = FALSE)
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48 annotation_input = input_tabular[,c($tabular_annotation.column_x, $tabular_annotation.column_y, $tabular_annotation.column_names)]
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49 annotation_name = colnames(annotation_input)[3] ##extract header for annotations to later export tabular with same name
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50 colnames(annotation_input) = c("x", "y", "annotation") ## rename annotations header to default name "annotation"
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51
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52 ## merge with coordinate information of msidata
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53 msidata_coordinates = cbind(coord(msidata)[,1:2], c(1:ncol(msidata)))
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54 colnames(msidata_coordinates)[3] = "pixel_index"
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55 merged_annotation = merge(msidata_coordinates, annotation_input, by=c("x", "y"), all.x=TRUE)
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56 merged_annotation[is.na(merged_annotation)] = "NA"
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57 merged_annotation = merged_annotation[order(merged_annotation\$pixel_index),]
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58 msidata\$annotation = as.factor(merged_annotation[,4])
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59
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60 #end if
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61
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62 ###################### calculation of data properties ################################
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63 @DATA_PROPERTIES_INRAM@
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64
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65 ## Median intensities
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66 medint = round(median(spectra(msidata), na.rm=TRUE), digits=2)
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67 ## Spectra multiplied with m/z (potential number of peaks)
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68 numpeaks = ncol(msidata)*nrow(msidata)
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69 ## Percentage of intensities > 0
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70 percpeaks = round(npeaks/numpeaks*100, digits=2)
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71 ## Number of empty TICs
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72 TICs = colSums(spectra(msidata), na.rm=TRUE)
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73 NumemptyTIC = sum(TICs == 0)
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74 ## Median und sd TIC
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75 medTIC = round(median(TICs), digits=1)
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76 sdTIC = round(sd(TICs), digits=0)
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77 ## Median and sd # peaks per spectrum
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78 medpeaks = round(median(colSums(spectra(msidata)>0, na.rm=TRUE), na.rm=TRUE), digits=0)
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79 sdpeaks = round(sd(colSums(spectra(msidata)>0, na.rm=TRUE), na.rm=TRUE), digits=0)
0
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80 ## Processing informations
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81 centroidedinfo = centroided(msidata)
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82
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83 ############## Read and filter tabular file with m/z ###########################
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84
2
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85 ### reading m/z input (calibrant) file:
0
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86
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87 #if $calibrant_file:
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88
2
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89 calibrant_list = read.delim("$calibrant_file", header = $calibrant_header, na.strings=c(" ","","NA"), stringsAsFactors = FALSE)
0
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90 calibrant_list = calibrant_list[,c($mz_column, $name_column)]
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91
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92 ### calculate how many input calibrant m/z are valid:
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93
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94 inputcalibrants = calibrant_list[calibrant_list[,1]>minmz & calibrant_list[,1]<maxmz,]
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95 number_calibrants_in = length(calibrant_list[,1])
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96 number_calibrants_valid = length(inputcalibrants[,1])
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97
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98 #else
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99
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100 inputcalibrants = as.data.frame(matrix(, nrow = 0, ncol = 2))
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101 number_calibrants_in = 0
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102 number_calibrants_valid = 0
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103
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104 #end if
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105
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106 ## rename input dataframe and extract m/z
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107 colnames(inputcalibrants) = c("m/z", "name")
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108 inputcalibrantmasses = inputcalibrants[,1]
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109
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110
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111 ######################################## PDF #############################################
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112 ##########################################################################################
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113 ##########################################################################################
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114
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115 pdf("qualitycontrol.pdf", fonts = "Times", pointsize = 12)
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116 plot(0,type='n',axes=FALSE,ann=FALSE)
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117
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118 ## if no filename is given, name of file in Galaxy history is used
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119
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120 #if not $filename:
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121 #set $filename = $infile.display_name
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122 #end if
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123
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124 title(main=paste("$filename"))
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125
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126 ################# I) file properties in numbers ################################
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127 ################################################################################
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128 print("properties in numbers")
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129
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130 properties2 = c("Median of intensities",
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131 "Intensities > 0",
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132 "Number of empty spectra",
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133 "Median TIC ± sd",
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134 "Median # peaks per spectrum ± sd",
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135 "Centroided",
2
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136 paste0("input m/z (#valid/#input) in \n", "$calibrant_file.display_name"))
0
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137
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138 values2 = c(paste0(medint),
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139 paste0(percpeaks, " %"),
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140 paste0(NumemptyTIC),
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141 paste0(medTIC, " ± ", sdTIC),
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142 paste0(medpeaks, " ± ",sdpeaks),
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143 paste0(centroidedinfo),
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144 paste0(number_calibrants_valid, " / ", number_calibrants_in))
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145
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146 property_df2 = data.frame(properties2, values2)
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147 colnames(property_df2) = c("properties", "values")
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148
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149 property_df = rbind(property_df, property_df2)
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150
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151 grid.table(property_df, rows= NULL)
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152
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153
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154 ####################### II) x-y images #######################################
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155 ##############################################################################
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156 print("x-y images")
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157
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158 ## only do plots for file with intensity peaks
2
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159
0
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160 if (npeaks > 0){
2
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161
0
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162 ## function for density plots
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163 plot_colorByDensity = function(x1,x2,
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164 ylim=c(min(x2),max(x2)),
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165 xlim=c(min(x1),max(x1)),
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166 xlab="",ylab="",main=""){
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167 df = data.frame(x1,x2)
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168 x = densCols(x1,x2, colramp=colorRampPalette(c("black", "white")))
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169 df\$dens = col2rgb(x)[1,] + 1L
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170 cols = colorRampPalette(c("#000099", "#00FEFF", "#45FE4F","#FCFF00", "#FF9400", "#FF3100"))(256)
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171 df\$col = cols[df\$dens]
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172 plot(x2~x1, data=df[order(df\$dens),], ylim=ylim,xlim=xlim,pch=20,col=col,
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173 cex=1,xlab=xlab,ylab=ylab,las=1, main=main)}
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174
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175
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176 ################### 0) overview for combined data ###########################
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177
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178 ### 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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179
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180 if (!is.null(levels(msidata\$annotation))){
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181
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182 number_combined = length(levels(msidata\$annotation))
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183
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184 position_df = cbind(coord(msidata)[,1:2], msidata\$annotation)
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185 colnames(position_df)[3] = "annotation"
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186
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187 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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188 geom_tile() +
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189 coord_fixed()+
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190 ggtitle("Spatial orientation of pixel annotations")+
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191 theme_bw()+
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192 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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193 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
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194 theme(legend.position="bottom",legend.direction="vertical")+
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195 guides(fill=guide_legend(ncol=4,byrow=TRUE))
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196
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197 print(combine_plot)
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198
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199 ## for each annotation group find last pixel, there dashed lines will be drawn in plots over spectra index
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200 pixel_name_df = data.frame(pixels(msidata), msidata\$annotation)
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201 colnames(pixel_name_df) = c("pixel_number", "pixel_name")
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202 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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203 pixel_vector = last_pixel[,2]
2
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204 abline_vector = pixel_vector
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205
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206 ## remove position_df to clean up RAM space
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207 rm(position_df)
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208 gc()
0
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209 }
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210
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211 ################### 1) Pixel order image ###################################
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212
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213 pixelnumber = 1:pixelcount
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214 pixelxyarray=cbind(coord(msidata)[,1:2],pixelnumber)
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215 gg_title = "Pixel order"
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216
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217 print(ggplot(pixelxyarray, aes(x=x, y=y, fill=pixelnumber))+
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218 geom_tile() + coord_fixed()+
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219 ggtitle(gg_title) + theme_bw()+
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220 theme(plot.title = element_text(hjust = 0.5))+
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221 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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222 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange"),
2
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223 space = "Lab", na.value = "black", name = "Pixel\nnumber"))
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224
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225 ## remove pixelxyarray to clean up RAM space
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226 rm(pixelxyarray)
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227 gc()
0
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228
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229 ################ 2) Number of calibrants per spectrum ######################
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230
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231 ## matrix with calibrants in columns and in rows if there is peak intensity in range or not
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232 pixelmatrix = matrix(ncol=ncol(msidata), nrow = 0)
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233
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234 ## plot only possible when there is at least one valid calibrant
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235 if (length(inputcalibrantmasses) != 0){
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236
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237 ## calculate plusminus values in m/z for each calibrant
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238 plusminusvalues = rep($plusminus_ppm/1000000, length(inputcalibrantmasses))*inputcalibrantmasses
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239
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240 ## filter for m/z window of each calibrant and calculate if sum of peak intensities > 0
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241
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242 for (mass in 1:length(inputcalibrantmasses)){
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243
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244 filtered_data = msidata[mz(msidata) >= inputcalibrantmasses[mass]-plusminusvalues[mass] & mz(msidata) <= inputcalibrantmasses[mass]+plusminusvalues[mass],]
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245
4
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246 if (nrow(filtered_data) > 1 & sum(spectra(filtered_data),na.rm=TRUE) > 0){
0
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247
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248 ## intensity of all m/z > 0
4
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249 intensity_sum = colSums(spectra(filtered_data), na.rm=TRUE) > 0
0
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250
4
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251 }else if(nrow(filtered_data) == 1 & sum(spectra(filtered_data), na.rm=TRUE) > 0){
0
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252
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253 ## intensity of only m/z > 0
4
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254 intensity_sum = spectra(filtered_data) > 0
0
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255
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256 }else{
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257
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258 intensity_sum = rep(FALSE, ncol(filtered_data))}
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259
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260 ## for each pixel add sum of intensities > 0 in the given m/z range
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261 pixelmatrix = rbind(pixelmatrix, intensity_sum)
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262 }
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263
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264 ## for each pixel count TRUE (each calibrant m/z range with intensity > 0 is TRUE)
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265 countvector= as.factor(colSums(pixelmatrix, na.rm=TRUE))
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266 countdf= cbind(coord(msidata)[,1:2], countvector) ## add pixel coordinates to counts
2
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267 mycolours = brewer.pal(9, "Set1")
0
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268
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269 print(ggplot(countdf, aes(x=x, y=y, fill=countvector))+
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270 geom_tile() + coord_fixed() +
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271 ggtitle(paste0("Number of calibrants per pixel (±",$plusminus_ppm, " ppm)")) +
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272 theme_bw() +
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273 theme(plot.title = element_text(hjust = 0.5))+
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274 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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275 scale_fill_manual(values = mycolours[1:length(countvector)],
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276 na.value = "black", name = "# calibrants"))
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277
2
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278 ## remove countdf to clean up RAM space
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279 rm(countdf)
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280 gc()
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281
0
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282 }else{print("2) The inputcalibrant m/z were not provided or outside the m/z range")}
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283
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284 ########################## 3) fold change image ###########################
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285
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286 #if $calibrantratio:
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287 #for $foldchanges in $calibrantratio:
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288 mass1 = $foldchanges.mass1
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289 mass2 = $foldchanges.mass2
2
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290 distance1 = $foldchanges.distance/1000000 * mass1
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291 distance2 = $foldchanges.distance/1000000 * mass2
0
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292
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293 ### if user did not write a label use input m/z as label
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294 #if not str($foldchanges.filenameratioplot).strip():
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295 #set $label = "log2 fold change %s Da / %s Da" % ($foldchanges.mass1, $foldchanges.mass2)
0
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296 #else:
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297 #set $label = $foldchanges.filenameratioplot
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298 #end if
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299
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300 ### filter msidata for given m/z range (for both input m/z)
2
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301 filtered_data1 = msidata[mz(msidata) >= mass1-distance1 & mz(msidata) <= mass1+distance1,]
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302 filtered_data2 = msidata[mz(msidata) >= mass2-distance2 & mz(msidata) <= mass2+distance2,]
0
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303 ### m/z range for each plot (fixed range of 5 Da)
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304 ### xlim does not work because it does not adjust for the max. intensities within the range
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305 mzdown1 = features(msidata, mz = mass1-2)
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306 mzup1 = features(msidata, mz = mass1+3)
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307 mzdown2 = features(msidata, mz = mass2-2)
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308 mzup2 = features(msidata, mz = mass2+3)
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309
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310 ### plot for first m/z
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311 par(mfrow=c(2,1), oma=c(0,0,2,0))
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312 plot(msidata[mzdown1:mzup1,], pixel = 1:pixelcount, main=paste0("Average spectrum ", mass1, " Da"))
2
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313 abline(v=c(mass1-distance1, mass1, mass1+distance1), col="blue",lty=c(3,6,3))
0
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314
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315 ### plot for second m/z
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316 plot(msidata[mzdown2:mzup2,], pixel = 1:pixelcount, main= paste0("Average spectrum ", mass2, " Da"))
2
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317 abline(v=c(mass2-distance2, mass2, mass2+distance2), col="blue", lty=c(3,6,3))
0
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318 title("Control of fold change plot", outer=TRUE)
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319
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320 ### filter spectra for max m/z to have two vectors, which can be divided
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321 ### plot spatial distribution of fold change
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322
2
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323 ## calculate mean intensity for each m/z over the ppm range; then calculate log2 foldchange
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324 mass1vector = colMeans(spectra(filtered_data1), na.rm =TRUE)
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325 mass2vector = colMeans(spectra(filtered_data2), na.rm = TRUE)
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326 foldchange= log2(mass1vector/mass2vector)
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327 fcmatrix = cbind(foldchange, coord(msidata)[,1:2])
0
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328
2
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329 print(ggplot(fcmatrix, aes(x=x, y=y, fill=foldchange))+
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330 geom_tile() + coord_fixed()+
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331 ggtitle("$label")+
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332 theme_bw()+
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333 theme(plot.title = element_text(hjust = 0.5))+
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334 theme(text=element_text(family="ArialMT", face="bold", size=12))+
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335 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
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336 ,space = "Lab", na.value = "black", name ="FC"))
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337
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338 ## remove FC files to clean up RAM space
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339 rm(fcmatrix)
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340 rm(filtered_data1)
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341 rm(filtered_data2)
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342 gc()
0
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343
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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344 #end for
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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345 #end if
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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346
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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347 #################### 4) m/z heatmaps #######################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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348
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
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349 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
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diff changeset
350 if (length(inputcalibrants[,1]) != 0){
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
351 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
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352
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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353
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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354 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
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355 main= paste0(inputcalibrants[,2][mass], ": ", round(inputcalibrants[,1][mass], digits = 2)," (±",$plusminus_ppm, " ppm)"),
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
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356 contrast.enhance = "histogram", ylim= c(maximumy+0.2*maximumy,minimumy-1))
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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357 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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358 } 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
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359
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
360 #################### 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:
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361
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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362 ## here every intensity value > 0 counts as peak
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
363 peaksperpixel = colSums(spectra(msidata)> 0, na.rm=TRUE)
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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364 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:
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365
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
366 print(ggplot(peakscoordarray, aes(x=x, y=y, fill=peaksperpixel))+
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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367 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
368 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
369 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
370 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
371 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
372 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
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diff changeset
373 ,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
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374
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
375 ## remove peakscoordarray to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
376 rm(peakscoordarray)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
377 gc()
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
378
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
379
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
380 ############################### 6) TIC image ###############################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
381
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
382 TICcoordarray=cbind(coord(msidata)[,1:2], TICs)
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
383
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
384 print(ggplot(TICcoordarray, aes(x=x, y=y, fill=TICs))+
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
385 geom_tile() + coord_fixed() +
5
f0d1f3e97303 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents: 4
diff changeset
386 ggtitle("Total Ion Current")+
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
387 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
388 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
389 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
390 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
391 ,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
392
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
393 ## remove TICcoordarray to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
394 rm(TICcoordarray)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
395 gc()
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
396
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
397 ############################### 6b) median int image ###############################
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
398
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
399 median_int = apply(spectra(msidata),2,median)
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
400 median_coordarray=cbind(coord(msidata)[,1:2], median_int)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
401
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
402 print(ggplot(median_coordarray, aes(x=x, y=y, fill=median_int))+
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
403 geom_tile() + coord_fixed() +
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
404 ggtitle("Median intensity per spectrum")+
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
405 theme_bw() +
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
406 theme(plot.title = element_text(hjust = 0.5))+
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
407 theme(text=element_text(family="ArialMT", face="bold", size=12))+
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
408 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
409 ,space = "Lab", na.value = "black", name = "median\nintensity"))
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
410
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
411 ## remove median_coordarray to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
412 rm(median_coordarray)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
413 gc()
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
414
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
415 ############################### 6c) max int image ###############################
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
416
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
417 max_int = apply(spectra(msidata),2,max)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
418 max_coordarray=cbind(coord(msidata)[,1:2], max_int)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
419
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
420 print(ggplot(max_coordarray, aes(x=x, y=y, fill=max_int))+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
421 geom_tile() + coord_fixed() +
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
422 ggtitle("Maximum intensity per spectrum")+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
423 theme_bw() +
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
424 theme(plot.title = element_text(hjust = 0.5))+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
425 theme(text=element_text(family="ArialMT", face="bold", size=12))+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
426 scale_fill_gradientn(colours = c("blue", "purple" , "red","orange")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
427 ,space = "Lab", na.value = "black", name = "max\nintensity"))
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
428
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
429 ## remove median_coordarray to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
430 rm(max_coordarray)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
431 gc()
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
432
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
433 ############################### 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
434
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
435 ## for each spectrum find the row (m/z) with the highest intensity
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
436 highestmz = apply(spectra(msidata),2,which.max)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
437 ## in case for some spectra max returns integer(0), highestmz is a list and integer(0) have to be replaced with NA and unlisted
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
438 if (class(highestmz) == "list"){
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
439 ##find zero-length values
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
440 zero_entry <- !(sapply(highestmz, length))
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
441 ### replace these values with NA
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
442 highestmz[zero_entry] <- NA
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
443 ### unlist list to get a vector
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
444 highestmz = unlist(highestmz)}
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
445
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
446 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
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diff changeset
447 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
448
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
449 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
450 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
451 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
452 theme_bw() +
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
453 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
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diff changeset
454 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
455 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
456 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
457
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
458 ## remove highestmz_matrix to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
459 rm(highestmz_matrix)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
460 gc()
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
461
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
462
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
463 ########################## 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
464
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
465 #if $do_pca:
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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466
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
467 set.seed(1)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
468 pca = PCA(msidata, ncomp=2)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
469
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
470 ## plot overview image and plot and PC1 and 2 images
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
471 par(mfrow = c(2,1))
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
472 plot(pca, col=c("black", "darkgrey"), main="PCA for two components")
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
473 image(pca, col=c("black", "white"), strip=FALSE, ylim= c(maximumy+0.2*maximumy,minimumy-1))
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
474
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
475 for (PCs in 1:2){
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
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diff changeset
476 print(image(pca, column = c(paste0("PC",PCs)) , strip=FALSE, superpose = FALSE, main=paste0("PC", PCs), col.regions = risk.colors(100), ylim=c(maximumy+2, minimumy-2)))}
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
477
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
478 ## remove pca to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
479 rm(pca)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
480 gc()
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
481
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
482 #end if
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
483
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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484 ################## 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
485 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
486 print("properties over pixels")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
487 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
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diff changeset
488
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
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489 ########################## 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
490 ## 9a) scatterplot
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:
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492 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
493 title(xlab="Spectra index", line=3)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
494 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
495
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
496 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
497 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
498
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
499 ## 9b) histogram
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 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
502 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
503 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
504 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
505
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
506 ## 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
507
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
508 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
509
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
510 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
511 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
512
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
513 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
514 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
515 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
516 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
517 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
518 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
519 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
520 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
521 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
522 print(hist_9)}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
523
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
524 ########################## 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
525
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
526 ## 10a)density scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
527 par(mfrow = c(2,1), mar=c(5,6,4,2))
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
528
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
529 ## colorDensityplot does not work after TIC normalization, therefore make normal plot
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
530 if (min(TICs) == max(TICs)){
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
531 plot(pixels(msidata), TICs, ylab = "", xlab = "", pch=20, main="TIC per spectrum", col="#FF3100")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
532 }else{
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
533 plot_colorByDensity(pixels(msidata), TICs, ylab = "", xlab = "", main="TIC per spectrum")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
534 }
0
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 title(xlab="Spectra index", line=3)
5
f0d1f3e97303 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents: 4
diff changeset
537 title(ylab = "Total ion current intensity", line=4)
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
538 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
539 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
540
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
541 ## 10b) histogram
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
542 hist((TICs), main="", las=1, xlab = "TIC per spectrum", ylab="")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
543 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
544 title(ylab="Frequency = # spectra", line=4)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
545 abline(v=median(TICs[TICs>0]), col="blue")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
546
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
547 ## 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
548 if (!is.null(levels(msidata\$annotation))){
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
549 df_10 = data.frame((TICs), msidata\$annotation)
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
550 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
551
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
552 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
553 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
554 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
555 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
556 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
557 theme(legend.key.size = unit(0.2, "line"), legend.text = element_text(size = 8))+
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
558 labs(title="TIC per spectrum and annotation group", x="TIC per spectrum", y = "Frequency = # spectra") +
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
559 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
560 geom_vline(xintercept = median(TICs[TICs>0]), size = 1, colour = "black",linetype = "dashed")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
561 print(hist_10)}
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 ################################## 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
564 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
565 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
566
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
567 ########################## 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
568
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
569 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
570 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
571
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
572 ########################## 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
573
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
574 peakspermz = rowSums(spectra(msidata) > 0, na.rm=TRUE)
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
575
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
576 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
577 ## 12a) scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
578 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
579 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
580 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
581 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
582 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
583
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
584 ## 12b) histogram
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
585 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
586 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
587 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
588 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
589
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
590 ########################## 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
591
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
592 ## Sum of all intensities for each m/z (like TIC, but for m/z instead of pixel)
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
593 mzTIC = rowSums(spectra(msidata), na.rm=TRUE) ## calculate intensity sum for each m/z
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
594
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
595 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
596 ## 13a) scatterplot
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
597 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
598 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
599 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
600
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
601 ## 13b) histogram
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
602 hist(mzTIC, main="", xlab = "", las=1, ylab="")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
603 title(main="Sum of intensities per m/z", line=2, ylab="")
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
604 title(xlab = "sum of intensities per m/z")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
605 title(ylab = "Frequency", line=4)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
606 abline(v=median(mzTIC[mzTIC>0]), col="blue")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
607
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
608 ################################## V) intensity plots ########################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
609 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
610 print("intensity plots")
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
611 ########################## 14) Intensity distribution ######################
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 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
614
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
615 ## 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
616
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
617 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
618 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
619 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
620 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
621 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
622
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
623 ## 14b) histogram:
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
624 hist(spectra(msidata), main="", xlab = "", ylab="", las=1)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
625 title(main="Intensity histogram", line=2)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
626 title(xlab="intensities")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
627 title(ylab="Frequency", line=4)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
628 abline(v=median(spectra(msidata)[(spectra(msidata)>0)], na.rm=TRUE), col="blue")
0
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
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
631 ## 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
632
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
633 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
634
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
635 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
636 for (subsample in levels(msidata\$annotation)){
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
637 log2_int_subsample = spectra(msidata)[,msidata\$annotation==subsample]
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
638 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
639 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
640 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
641 df_13\$annotation = as.factor(df_13\$annotation)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
642 colnames(df_13) = c("int", "annotation")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
643
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
644 hist_13 = ggplot(df_13, aes(x=int, fill=annotation)) +
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
645 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
646 theme(text=element_text(family="ArialMT", face="bold", size=12))+
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
647 labs(title="Intensities per sample", x="intensities", y = "Frequency") +
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
648 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
649 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
650 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
651 guides(fill=guide_legend(ncol=5,byrow=TRUE))+
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
652 geom_vline(xintercept = median(spectra(msidata)[(spectra(msidata)>0)]), size = 1, colour = "black",linetype = "dashed")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
653 print(hist_13)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
654
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
655 ## 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
656 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
657
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
658 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
659 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
660 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
661 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
662
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
663 boxplot(log10(mean_matrix), ylab = "Log10 mean intensity per m/z", main="Log10 mean m/z intensities per annotation group", xaxt = "n")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
664 (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
665
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
666 ## 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
667
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
668 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
669 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
670 colnames(corr_matrix) = levels(msidata\$annotation)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
671 ## pearson correlation is only possible if there are at least 2 groups
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
672 if (length(colnames)>1)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
673 {
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
674 corr_matrix = cor(corr_matrix, method= "pearson",use="complete.obs")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
675
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
676 heatmap.parameters <- list(corr_matrix,
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
677 show_rownames = T, show_colnames = T,
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
678 main = "Pearson correlation on mean intensities")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
679 do.call("pheatmap", heatmap.parameters)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
680 }
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
681 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
682
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
683 ################################## 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
684 ############################################################################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
685 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
686
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
687 ############################ 15) Mass spectra ##############################
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
688
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
689 ## 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
690 msidata_no_NA = msidata
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
691 spectra(msidata_no_NA)[is.na(spectra(msidata_no_NA))] = 0
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
692
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
693 ## find three equal m/z ranges for the average mass spectra plots:
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
694 third_mz_range = nrow(msidata_no_NA)/3
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
695
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
696 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
697 plot(msidata_no_NA, pixel = 1:ncol(msidata_no_NA), main= "Average spectrum")
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
698 plot(msidata_no_NA[1:third_mz_range,], pixel = 1:ncol(msidata_no_NA), main= "Zoomed average spectrum")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
699 plot(msidata_no_NA[third_mz_range:(2*third_mz_range),], pixel = 1:ncol(msidata_no_NA), main= "Zoomed average spectrum")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
700 plot(msidata_no_NA[(2*third_mz_range):nrow(msidata_no_NA),], pixel = 1:ncol(msidata_no_NA), main= "Zoomed average spectrum")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
701
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
702 ## plot one average mass spectrum for each pixel annotation group
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
703
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
704 if (!is.null(levels(msidata\$annotation))){
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
705 ## print legend only for less than 10 samples
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
706 if (length(levels(msidata\$annotation)) < 10){
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
707 key_legend = TRUE
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
708 }else{key_legend = FALSE}
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
709 par(mfrow = c(1,1), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
710 plot(msidata, pixel=1:ncol(msidata), pixel.groups=msidata\$annotation, key=key_legend, col=hue_pal()(length(levels(msidata\$annotation))),superpose=TRUE, main="Average mass spectra for annotation groups")
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
711 }
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
712
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
713 ## plot 4 random mass spectra
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
714 ## find four random pixel to plot their spectra in the following plots:
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
715 pixel1 = sample(pixelnumber,1)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
716 pixel2 = sample(pixelnumber,1)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
717 pixel3 = sample(pixelnumber,1)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
718 pixel4 = sample(pixelnumber,1)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
719
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
720 par(mfrow = c(2, 2), cex.axis=1, cex.lab=1, mar=c(5.1,4.1,4.1,2.1))
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
721 plot(msidata_no_NA, pixel = pixel1, main=paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel1,1:2])))
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
722 plot(msidata_no_NA, pixel = pixel2, main=paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel2,1:2])))
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
723 plot(msidata_no_NA, pixel = pixel3, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel3,1:2])))
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
724 plot(msidata_no_NA, pixel = pixel4, main= paste0("Spectrum at ", rownames(coord(msidata_no_NA)[pixel4,1:2])))
0
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 ################### 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
727
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
728 count = 1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
729 differencevector = numeric()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
730 differencevector2 = vector()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
731
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
732 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
733
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
734 ### 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
735 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
736
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
737 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
738
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
739 ### define the plot window with xmin und xmax
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
740 minmasspixel1 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-0.5)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
741 maxmasspixel1 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+1.5)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
742 minmasspixel2 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-0.25)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
743 maxmasspixel2 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+0.5)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
744 minmasspixel3 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]-3)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
745 maxmasspixel3 = features(msidata_no_NA, mz=inputcalibrantmasses[mass]+3)
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
746
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
747 ### 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
748 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
749
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
750 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
751 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
752 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
753 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
754 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
755 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
756 ppmdifference = NA
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
757 maxvalue = NA}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
758 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
759
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
760 ### 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
761 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
762 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
763 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
764 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
765 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
766
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
767 ## plotting of 4 spectra in one page
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
768 par(mfrow = c(2, 2), oma=c(0,0,2,0))
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
769 ## average plot
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
770 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main= "Average spectrum")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
771 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
772 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
773 abline(v=c(mzvalue), col="green2", lty=4)
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
774 ## average plot including points per data point
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
775 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel = 1:length(pixelnumber), main="Average spectrum with data points")
5
f0d1f3e97303 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents: 4
diff changeset
776 points(mz(msidata_no_NA[minmasspixel1:maxmasspixel1,]), rowMeans(spectra(msidata_no_NA)[minmasspixel1:maxmasspixel1,,drop=FALSE]), col="blue", pch=20)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
777 ## plot of third average plot
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
778 plot(msidata_no_NA[minmasspixel2:maxmasspixel2,], pixel = 1:length(pixelnumber), main= "Average spectrum")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
779 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
780 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
781 abline(v=c(mzvalue), col="green2", lty=4)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
782 ## plot of fourth average plot
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
783 plot(msidata_no_NA[minmasspixel3:maxmasspixel3,], pixel = 1:length(pixelnumber), main= "Average spectrum")
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
784 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
785 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
786 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
787 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
788 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
789 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
790
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
791 ### 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
792
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
793 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
794 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
795 key_zoomed = TRUE
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
796 }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
797 par(mfrow = c(1, 1))
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
798 plot(msidata_no_NA[minmasspixel1:maxmasspixel1,], pixel=1:ncol(msidata_no_NA),main="Average spectrum per annotation group",
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
799 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
800 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
801 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
802 count=count+1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
803 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
804
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
805 ## remove msidata_no_NA to clean up RAM space
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
806 rm(msidata_no_NA)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
807 gc()
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
808
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
809 ######### 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
810
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
811 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
812 ### 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
813
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
814 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
815 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
816
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
817 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
818 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
819 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
820 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
821
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
822 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
823 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
824 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
825 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
826 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
827
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
828 print(diff_plot1)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
829 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
830
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
831 ######### 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
832
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
833 ### 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
834
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
835 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
836 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
837 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
838
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
839 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
840 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
841 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
842 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
843 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
844
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
845 print(diff_plot2)
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
846
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
847 #################### 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
848
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
849 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
850 count = 1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
851 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
852 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
853 ### 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
854 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
855
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
856 if (nrow(filtered_data) > 0){
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
857 ### filtered for m/z range, find max peak in each spectrum
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
858 ppm_vector = numeric()
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
859 for (pixel_count in 1:ncol(filtered_data)){
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
860 ## for each spectrum (pixel_count) find the m/z that has the highest intensity
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
861 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
862 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
863 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
864
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
865 ### if maximum intensity in m/z range was 0 set ppm diff to NA (not shown in plot)
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
866 if (max(spectra(filtered_data)[,pixel_count]) == 0 || is.na(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
867 ppmdiff = NA}
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
868 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
869
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
870 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
871 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
872 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
873
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
874 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
875 count=count+1
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
876 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
877
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
878 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
879 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
880 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
881 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
882
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
883 ### plot ppm differences over pixels (spectra index)
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
884 par(mar=c(4.1, 4.1, 4.1, 8.5))
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
885
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
886 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
887 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
888 lines(ppm_df[,each_cal], col=mycolours[each_cal], type="p")}
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
889 legend("topright", inset=c(-0.2,0), xpd = TRUE, bty="n", cex=0.8,legend=inputcalibrantmasses, col=mycolours[1:ncol(ppm_df)],lty=1)
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
890 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
891 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
892
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
893 ### make x-y-images for mz accuracy
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
894
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
895 ppm_dataframe = cbind(coord(msidata)[,1:2], ppm_df)
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
896
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
897 for (each_cal in 1:ncol(ppm_df)){
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
898 tmp_ppm = ppm_dataframe[,c(1,2,each_cal+2)]
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
899 tmp_ppm[,3] = as.numeric(tmp_ppm[,3])
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
900 colnames(tmp_ppm) = c("x","y", "ppm_each_cal")
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
901
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
902 print(ggplot(tmp_ppm, aes(x=x, y=y, fill=ppm_each_cal))+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
903 geom_tile() + coord_fixed() +
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
904 ggtitle(paste0("m/z accuracy for ",inputcalibrants[,2][each_cal]))+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
905 theme_bw() +
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
906 theme(plot.title = element_text(hjust = 0.5))+
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
907 theme(text=element_text(family="ArialMT", face="bold", size=12))+
3
16556ca0196b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
908 scale_fill_gradient2(low = "navy", mid = "grey", high = "red", midpoint = 0 ,space = "Lab", na.value = "black", name = "ppm\nerror"))}
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
909
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
910
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
911 }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
912 }else{
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
913 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
914 }
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
915 dev.off()
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
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
918 ]]></configfile>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
919 </configfiles>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
920 <inputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
921 <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
922 <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
923 <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
924 <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
925 <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
926 </param>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
927 <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
928 <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
929 </when>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
930 <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
931 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
932 <expand macro="pdf_filename"/>
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
933 <expand macro="reading_2_column_mz_tabular" optional="true"/>
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
934 <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
935 <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
936 <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
937 <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
938 <param name="mass2" value="2222" type="float" label="M/z 2" help="Second m/z"/>
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
939 <param name="distance" value="200" type="float" label="ppm range" help="Will be added in both directions to input calibrant m/z and intensities will be averaged in this range."/>
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
940 <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
941 <sanitizer invalid_char="">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
942 <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
943 <add value="_" />
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
944 </valid>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
945 </sanitizer>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
946 </param>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
947 </repeat>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
948 </inputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
949 <outputs>
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
950 <data format="pdf" name="QC_report" from_work_dir="qualitycontrol.pdf" label = "${tool.name} on ${on_string}: results"/>
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
951 </outputs>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
952 <tests>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
953 <test>
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
954 <param name="infile" value="" ftype="imzml">
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
955 <composite_data value="Example_Processed.imzML"/>
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
956 <composite_data value="Example_Processed.ibd"/>
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
957 </param>
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
958 <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
959 <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
960 <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
961 <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
962 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
963 <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
964 <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
965 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
966 <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
967 <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
968 <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
969 <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
970 <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
971 <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
972 <repeat name="calibrantratio">
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
973 <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
974 <param name="mass2" value="398.8"/>
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
975 <param name="distance" value="500"/>
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
976 <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
977 </repeat>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
978 <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
979 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
980
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
981 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
982 <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
983 <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
984 <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
985 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
986 <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
987 <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
988 <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
989 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
990
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
991 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
992 <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
993 <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
994 <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
995 <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
996 <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
997 <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
998 <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
999 <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
1000 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1001 <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
1002 <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
1003 <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
1004 <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
1005 <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
1006 <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
1007 <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
1008 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1009 <test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1010 <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
1011 <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
1012 <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
1013 </conditional>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1014 <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
1015 <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
1016 <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
1017 <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
1018 <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
1019 <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
1020 </test>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1021 </tests>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1022 <help>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1023 <![CDATA[
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1024 @CARDINAL_DESCRIPTION@
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1025
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1026 -----
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1027
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1028 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
1029
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1030 @MSIDATA_INPUT_DESCRIPTION@
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1031 - 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
1032 @SPECTRA_TABULAR_INPUT_DESCRIPTION@
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1033 - at least two different annotations should be in the annotation column
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1034
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1035 @MZ_2COLS_TABULAR_INPUT_DESCRIPTION@
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1036 - maximum of 9 m/z values per run are supported
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1037 - names should be unique
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1038
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1039 **Options**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1040
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1041 - 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
1042 - 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
1043 - 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
1044
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1045 **Tip**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1046
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1047 - 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
1048 - 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
1049
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1050
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1051 **Output**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1052
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1053 - 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
1054
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1055
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1056 ----------------------------------------------------------------------------------------------------------------------------------------------------
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1057
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1058 **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
1059
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1060 - (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
1061 - (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
1062 - (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
1063 - 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
1064
5
f0d1f3e97303 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents: 4
diff changeset
1065 - 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 current) 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).
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1066
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1067 **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
1068
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1069 - (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
1070 - 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
1071 - (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
1072 - (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.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1073 - (FC) Fold change image: For each input m/z the average intensity within the given ppm range is calculated, then the log2 fold change of both average intensities is taken and plotted as heatmap.
3
16556ca0196b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 2c4a1a862900b4efbc30824cbcb798f835b168b2
galaxyp
parents: 2
diff changeset
1074 - (cal) Intensity heatmaps for the m/z value that is closest to the calibrant m/z (can be outside the ppm range). The intensities are averaged within the calibrant m/z window (ppm range).
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1075 - Number of peaks per spectrum: For each spectrum the number of m/z values with intensity > 0 is calculated and plotted as heatmap.
5
f0d1f3e97303 "planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit e938d5bf0087479d893ac3889db4ea5ef87a471c"
galaxyp
parents: 4
diff changeset
1076 - Total ion current: For each spectrum all intensities are summed up to obtain the TIC which is plotted as heatmap.
1
ae9ffc7ba261 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit d2f311f7fff24e54c565127c40414de708e31b3c
galaxyp
parents: 0
diff changeset
1077 - Median intensity: For each spectrum the median intensity is plotted as heatmap.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1078 - Maximum intensity: For each spectrum the maximum intensity is plotted as heatmap.
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1079 - Most abundant m/z in each spectrum: For each spectrum the m/z value with the highest intensity is plotted.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1080 - 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, principal components 1 and 2 are also plotted as x-y image.
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1081
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1082 **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
1083
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1084 - 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
1085 - (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
1086 - 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.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1087 - (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. Only the length of the coloured bar is important and not its height from zero, as bars are added up and not overlayed.
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1088
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1089 **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
1090
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1091 - 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
1092 - 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
1093 - 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
1094
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1095 **Intensity plots**
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1096
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1097 - 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.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1098 - Histogram of intensities.
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1099 - (annot) Intensities per annotation group: Same histogram as before but with colours to show the contribution of each pixel annotation group.
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1100 - (annot) Log10 mean intensities per m/z and annotation group: For all pixels of an annotation group the log10 mean intensity for each m/z is calculated and shown as boxplot.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1101 - (annot) Pearson correlation between annotation groups (needs at least 2 groups) based on mean intensities and shown as heatmap.
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1102
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1103 **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
1104
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1105 - Average mass spectra: First plot shows the average spectrum over the full m/z range, the other three plots zoom into the m/z axis.
4
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1106 - (annot) Average mass spectrum per annotation group.
3b7a35d50ebf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit ecdc3a64aa245d80dbc5487b2bf10a85a43adc6d
galaxyp
parents: 3
diff changeset
1107 - Random mass spectra: The mass spectra for four random pixel are plotted.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1108 - (cal) For each calibrant four zoomed average mass spectrum are drawn with different zooming level. 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. In the second spectrum each blue dot indicates one data point.
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1109 - (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
1110 - (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
1111 - (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
1112 - (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.
2
d4803c1e5e19 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit f127be2141cf22e269c85282d226eb16fe14a9c1
galaxyp
parents: 1
diff changeset
1113 - (cal) Same m/z accuracy in ppm is plotted per calibrant and per spectrum as image in x-y dimension.
0
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1114
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1115
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1116 ]]>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1117 </help>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
parents:
diff changeset
1118 <expand macro="citations"/>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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diff changeset
1119 </tool>
5f18275c250a planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cardinal commit 0825a4ccd3ebf4ca8a298326d14f3e7b25ae8415
galaxyp
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1120