Mercurial > repos > davidvanzessen > shm_csr
diff shm_csr.r @ 43:77a7ac76c7b9 draft
Uploaded
author | davidvanzessen |
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date | Tue, 11 Apr 2017 08:02:17 -0400 |
parents | 1cf60ae234b4 |
children | aa8d37bd1930 |
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--- a/shm_csr.r Tue Mar 28 08:25:36 2017 -0400 +++ b/shm_csr.r Tue Apr 11 08:02:17 2017 -0400 @@ -124,6 +124,8 @@ regions = c("CDR2", "FR3") } +pdfplots = list() #save() this later to create the pdf plots in another script (maybe avoids the "address (nil), cause memory not mapped") + sum_by_row = function(x, columns) { sum(as.numeric(x[columns]), na.rm=T) } print("aggregating data into new columns") @@ -308,7 +310,7 @@ print(p) dev.off() - ggsave(paste("transitions_stacked_", name, ".pdf", sep="")) + pdfplots[[paste("transitions_stacked_", name, ".pdf", sep="")]] <<- p png(filename=paste("transitions_heatmap_", name, ".png", sep="")) p = ggplot(transition2, aes(factor(reorder(variable, -order.y)), factor(reorder(id, -order.x)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap @@ -316,7 +318,7 @@ print(p) dev.off() - ggsave(paste("transitions_heatmap_", name, ".pdf", sep="")) + pdfplots[[paste("transitions_heatmap_", name, ".pdf", sep="")]] <<- p } else { #print("No data to plot") } @@ -400,7 +402,7 @@ print(pc) dev.off() - ggsave("IGA.pdf", pc) + pdfplots[["IGA.pdf"]] <- pc } print("Plotting IGG piechart") @@ -423,7 +425,7 @@ print(pc) dev.off() - ggsave("IGG.pdf", pc) + pdfplots[["IGG.pdf"]] <- pc } print("Plotting scatterplot") @@ -445,7 +447,7 @@ print(p) dev.off() -ggsave("scatter.pdf", p) +pdfplots[["scatter.pdf"]] <- p write.table(dat[,c("Sequence.ID", "best_match", "VRegionMutations", "VRegionNucleotides", "percentage_mutations")], "scatter.txt", sep="\t",quote=F,row.names=F,col.names=T) @@ -471,7 +473,9 @@ print(p) dev.off() -ggsave("frequency_ranges.pdf", p) +pdfplots[["frequency_ranges.pdf"]] <- p + +save(pdfplots, file="pdfplots.RData") frequency_bins_data_by_class = frequency_bins_data