Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 26:f35c127b29b1 draft

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author davidvanzessen
date Tue, 24 Feb 2015 11:19:26 -0500
parents 99020e5ce46c
children dd8518ea23dd
comparison
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25:99020e5ce46c 26:f35c127b29b1
347 filenameTwo_three = paste(label2, "_", label3, "_", product[iter, titleIndex], "_", threshhold, onShort, sep="") 347 filenameTwo_three = paste(label2, "_", label3, "_", product[iter, titleIndex], "_", threshhold, onShort, sep="")
348 write.table(dfTwo_three, file=paste(filenameTwo_three, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T) 348 write.table(dfTwo_three, file=paste(filenameTwo_three, ".txt", sep=""), quote=F, sep="\t", dec=",", row.names=F, col.names=T)
349 } 349 }
350 } else { #scatterplot data 350 } else { #scatterplot data
351 scatterplot_locus_data = scatterplot_data[grepl(V_Segment, scatterplot_data$V_Segment_Major_Gene) & grepl(J_Segment, scatterplot_data$J_Segment_Major_Gene),] 351 scatterplot_locus_data = scatterplot_data[grepl(V_Segment, scatterplot_data$V_Segment_Major_Gene) & grepl(J_Segment, scatterplot_data$J_Segment_Major_Gene),]
352 scatterplot_locus_data$type = ifelse(scatterplot_locus_data$Clone_Sequence %in% patientMerge12[one_two,]$Clone_Sequence.x, "In two", "In one") 352 scatterplot_locus_data$type = ifelse((scatterplot_locus_data$Clone_Sequence %in% patientMerge12[one_two,]$Clone_Sequence.x) | (scatterplot_locus_data$Clone_Sequence %in% patientMerge13[one_three,]$Clone_Sequence.x) | (scatterplot_locus_data$Clone_Sequence %in% patientMerge23[two_three,]$Clone_Sequence.x), "In two", "In one")
353 scatterplot_locus_data$type = ifelse(scatterplot_locus_data$Clone_Sequence %in% patientMerge13[one_three,]$Clone_Sequence.x, "In two", "In one") 353 #scatterplot_locus_data$type = ifelse(scatterplot_locus_data$type == "In two", ifelse(scatterplot_locus_data$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x, "In three", "In two"), "In one")
354 scatterplot_locus_data$type = ifelse(scatterplot_locus_data$Clone_Sequence %in% patientMerge23[two_three,]$Clone_Sequence.x, "In two", "In one") 354 scatterplot_locus_data[(scatterplot_locus_data$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x),]$type = "In three"
355 scatterplot_locus_data$type = ifelse(scatterplot_locus_data$type == "In two", ifelse(scatterplot_locus_data$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x, "In three", "In two"), "In one")
356 scatterplot_locus_data$type = ifelse(scatterplot_locus_data$type == "In one", "In one", "In multiple") 355 scatterplot_locus_data$type = ifelse(scatterplot_locus_data$type == "In one", "In one", "In multiple")
357 356
358 p = NULL 357 p = NULL
359 if(nrow(scatterplot_locus_data) != 0){ 358 if(nrow(scatterplot_locus_data) != 0){
360 if(on == "normalized_read_count"){ 359 if(on == "normalized_read_count"){