Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
changeset 28:a63ccc36f5a4 draft
Uploaded
author | davidvanzessen |
---|---|
date | Tue, 19 May 2015 08:13:49 -0400 |
parents | dd8518ea23dd |
children | 5ab17bdf2530 |
files | RScript.r script.js wrapper.sh |
diffstat | 1 files changed, 5 insertions(+), 3 deletions(-) [+] |
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--- a/RScript.r Wed Feb 25 09:18:14 2015 -0500 +++ b/RScript.r Tue May 19 08:13:49 2015 -0400 @@ -61,6 +61,9 @@ TitlesOrder = data.frame("Title"=Titles, "TitlesOrder"=1:length(Titles)) patientCountOnColumn <- function(x, product, interval, on, appendtxt=F){ + if (!is.data.frame(x) & is.list(x)){ + x = x[[1]] + } x$Sample = factor(x$Sample, levels=unique(x$Sample)) onShort = "reads" if(on == "Frequency"){ @@ -255,9 +258,8 @@ patientMerge = merge(patient1, patient2, by="merge") patientMerge = merge(patientMerge, patient3, by="merge") - colnames(patientMerge)[30:length(colnames(patientMerge))] = paste(colnames(patientMerge)[30:length(colnames(patientMerge))], ".z", sep="") + colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge)))] = paste(colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge), perl=T))], ".z", sep="") patientMerge$thresholdValue = pmax(patientMerge[,onx], patientMerge[,ony], patientMerge[,onz]) - patientMerge12 = merge(patient1, patient2, by="merge") patientMerge12$thresholdValue = pmax(patientMerge12[,onx], patientMerge12[,ony]) patientMerge13 = merge(patient1, patient3, by="merge") @@ -265,6 +267,7 @@ patientMerge23 = merge(patient2, patient3, by="merge") patientMerge23$thresholdValue = pmax(patientMerge23[,onx], patientMerge23[,ony]) + scatterplot_data_columns = c("Clone_Sequence", "Frequency", "normalized_read_count", "V_Segment_Major_Gene", "J_Segment_Major_Gene") scatterplot_data = rbind(patient1[,scatterplot_data_columns], patient2[,scatterplot_data_columns], patient3[,scatterplot_data_columns]) scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$Clone_Sequence),] @@ -358,7 +361,6 @@ scatterplot_locus_data[in_three,]$type = "In three" } not_in_one = scatterplot_locus_data$type != "In one" - print(not_in_one) if(sum(not_in_one) > 0){ scatterplot_locus_data[not_in_one,]$type = "In multiple" }