Mercurial > repos > lecorguille > xcms_export_samplemetadata

comparison lib.r @ 4:8c62030a1136 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit f0d42bca2f34c58c04b55e5990058d479c0ae639
author lecorguille
date Mon, 11 Feb 2019 06:16:45 -0500
parents 10f7b1548200
children 14316f8f67a2
comparison
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3:10f7b1548200 4:8c62030a1136
142 return (dataMatrix) 142 return (dataMatrix)
143 } 143 }
144 144
145 #@author G. Le Corguille 145 #@author G. Le Corguille
146 # Draw the plotChromPeakDensity 3 per page in a pdf file 146 # Draw the plotChromPeakDensity 3 per page in a pdf file
147 getPlotChromPeakDensity <- function(xdata, mzdigit=4) { 147 getPlotChromPeakDensity <- function(xdata, param = NULL, mzdigit=4) {
148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12) 148 pdf(file="plotChromPeakDensity.pdf", width=16, height=12)
149 149
150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5)) 150 par(mfrow = c(3, 1), mar = c(4, 4, 1, 0.5))
151 151
152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))] 152 group_colors <- brewer.pal(3, "Set1")[1:length(unique(xdata$sample_group))]
154 154
155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) 155 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
156 for (i in 1:nrow(featureDefinitions(xdata))) { 156 for (i in 1:nrow(featureDefinitions(xdata))) {
157 mzmin = featureDefinitions(xdata)[i,]$mzmin 157 mzmin = featureDefinitions(xdata)[i,]$mzmin
158 mzmax = featureDefinitions(xdata)[i,]$mzmax 158 mzmax = featureDefinitions(xdata)[i,]$mzmax
159 plotChromPeakDensity(xdata, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit))) 159 plotChromPeakDensity(xdata, param = param, mz=c(mzmin,mzmax), col=group_colors, pch=16, xlim=xlim, main=paste(round(mzmin,mzdigit),round(mzmax,mzdigit)))
160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) 160 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
161 } 161 }
162 162
163 dev.off() 163 dev.off()
164 } 164 }
187 #@author G. Le Corguille 187 #@author G. Le Corguille
188 # value: intensity values to be used into, maxo or intb 188 # value: intensity values to be used into, maxo or intb
189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) { 189 getPeaklistW4M <- function(xdata, intval="into", convertRTMinute=F, numDigitsMZ=4, numDigitsRT=0, naTOzero=T, variableMetadataOutput, dataMatrixOutput, sampleNamesList) {
190 dataMatrix <- featureValues(xdata, method="medret", value=intval) 190 dataMatrix <- featureValues(xdata, method="medret", value=intval)
191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix))) 191 colnames(dataMatrix) <- make.names(tools::file_path_sans_ext(colnames(dataMatrix)))
192 dataMatrix = cbind(name=groupnamesW4M(xdata), dataMatrix) 192 dataMatrix = cbind(name=groupnames(xdata), dataMatrix)
193 variableMetadata <- featureDefinitions(xdata) 193 variableMetadata <- featureDefinitions(xdata)
194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt" 194 colnames(variableMetadata)[1] = "mz"; colnames(variableMetadata)[4] = "rt"
195 variableMetadata = data.frame(name=groupnamesW4M(xdata), variableMetadata) 195 variableMetadata = data.frame(name=groupnames(xdata), variableMetadata)
196 196
197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute) 197 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ) 198 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero) 199 dataMatrix <- naTOzeroDataMatrix(dataMatrix, naTOzero)
200 200