Mercurial > repos > lecorguille > xcms_summary

comparison lib.r @ 27:bed23aa27b4b draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 50478425b4773ebcb393c0e31f1e622b7406dcbb"
author workflow4metabolomics
date Thu, 24 Sep 2020 08:09:02 +0000
parents db6549f27ad1
children 018a9771de28
comparison
equal deleted inserted replaced
26:db6549f27ad1 27:bed23aa27b4b
147 getPlotChromPeakDensity <- function(xdata, param = NULL, 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(length(unique(xdata$sample_group)), "Set1") 152 if(length(unique(xdata$sample_group))<10){
153 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
154 }else{
155 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
156 }
153 names(group_colors) <- unique(xdata$sample_group) 157 names(group_colors) <- unique(xdata$sample_group)
154 col_per_samp <- as.character(xdata$sample_group) 158 col_per_samp <- as.character(xdata$sample_group)
155 for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]} 159 for(i in 1:length(group_colors)){col_per_samp[col_per_samp==(names(group_colors)[i])]<-group_colors[i]}
156 160
157 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax)) 161 xlim <- c(min(featureDefinitions(xdata)$rtmin), max(featureDefinitions(xdata)$rtmax))
170 getPlotAdjustedRtime <- function(xdata) { 174 getPlotAdjustedRtime <- function(xdata) {
171 175
172 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12) 176 pdf(file="raw_vs_adjusted_rt.pdf", width=16, height=12)
173 177
174 # Color by group 178 # Color by group
175 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") 179 if(length(unique(xdata$sample_group))<10){
180 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
181 }else{
182 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
183 }
176 if (length(group_colors) > 1) { 184 if (length(group_colors) > 1) {
177 names(group_colors) <- unique(xdata$sample_group) 185 names(group_colors) <- unique(xdata$sample_group)
178 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group]) 186 plotAdjustedRtime(xdata, col = group_colors[xdata$sample_group])
179 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) 187 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
180 } 188 }
239 main <- paste(type,":",adjusted,"data") 247 main <- paste(type,":",adjusted,"data")
240 248
241 pdf(pdfname, width=16, height=10) 249 pdf(pdfname, width=16, height=10)
242 250
243 # Color by group 251 # Color by group
244 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1") 252 if(length(unique(xdata$sample_group))<10){
253 group_colors <- brewer.pal(length(unique(xdata$sample_group)), "Set1")
254 }else{
255 group_colors <- hcl.colors(length(unique(xdata$sample_group)), palette="Dark 3")
256 }
245 if (length(group_colors) > 1) { 257 if (length(group_colors) > 1) {
246 names(group_colors) <- unique(xdata$sample_group) 258 names(group_colors) <- unique(xdata$sample_group)
247 plot(chrom, col = group_colors[as.factor(chrom$sample_group)], main=main, peakType = "none") 259 plot(chrom, col = group_colors[chrom$sample_group], main=main, peakType = "none")
248 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1) 260 legend("topright", legend=names(group_colors), col=group_colors, cex=0.8, lty=1)
249 } 261 }
250 262
251 # Color by sample 263 # Color by sample
252 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none") 264 plot(chrom, col = rainbow(length(xdata@phenoData@data$sample_name)), main=main, peakType = "none")