Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 25:99020e5ce46c draft

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author davidvanzessen
date Tue, 24 Feb 2015 10:10:45 -0500
parents 6904186d13b9
children f35c127b29b1
comparison
equal deleted inserted replaced
24:6904186d13b9 25:99020e5ce46c
289 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="") 289 V_Segment = paste(".*", as.character(product[iter,V_SegmentIndex]), ".*", sep="")
290 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="") 290 J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
291 #all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,onx] > threshhold & patientMerge[,ony] > threshhold & patientMerge[,onz] > threshhold) 291 #all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,onx] > threshhold & patientMerge[,ony] > threshhold & patientMerge[,onz] > threshhold)
292 all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge$thresholdValue > threshhold) 292 all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge$thresholdValue > threshhold)
293 293
294 one_two = (grepl(V_Segment, patientMerge12$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge12$J_Segment_Major_Gene.x) & patientMerge12$thresholdValue > threshhold & !(patientMerge12$Clone_Sequence %in% patientMerge[all,]$merge)) 294 one_two = (grepl(V_Segment, patientMerge12$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge12$J_Segment_Major_Gene.x) & patientMerge12$thresholdValue > threshhold & !(patientMerge12$Clone_Sequence.x %in% patientMerge[all,]$merge))
295 one_three = (grepl(V_Segment, patientMerge13$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge13$J_Segment_Major_Gene.x) & patientMerge13$thresholdValue > threshhold & !(patientMerge13$Clone_Sequence %in% patientMerge[all,]$merge)) 295 one_three = (grepl(V_Segment, patientMerge13$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge13$J_Segment_Major_Gene.x) & patientMerge13$thresholdValue > threshhold & !(patientMerge13$Clone_Sequence.x %in% patientMerge[all,]$merge))
296 two_three = (grepl(V_Segment, patientMerge23$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge23$J_Segment_Major_Gene.x) & patientMerge23$thresholdValue > threshhold & !(patientMerge23$Clone_Sequence %in% patientMerge[all,]$merge)) 296 two_three = (grepl(V_Segment, patientMerge23$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge23$J_Segment_Major_Gene.x) & patientMerge23$thresholdValue > threshhold & !(patientMerge23$Clone_Sequence.x %in% patientMerge[all,]$merge))
297 297
298 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[all,]$merge) & !(patientMerge12$Clone_Sequence %in% patientMerge[all,]$merge) & !(patientMerge13$Clone_Sequence %in% patientMerge[all,]$merge)) 298 one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[all,]$merge) & !(patient1$Clone_Sequence %in% patientMerge12[one_two,]$merge) & !(patient1$Clone_Sequence %in% patientMerge13[one_three,]$merge))
299 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[all,]$merge) & !(patientMerge12$Clone_Sequence %in% patientMerge[all,]$merge) & !(patientMerge23$Clone_Sequence %in% patientMerge[all,]$merge)) 299 two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[all,]$merge) & !(patient2$Clone_Sequence %in% patientMerge12[one_two,]$merge) & !(patient2$Clone_Sequence %in% patientMerge23[two_three,]$merge))
300 three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$Clone_Sequence %in% patientMerge[all,]$merge) & !(patientMerge13$Clone_Sequence %in% patientMerge[all,]$merge) & !(patientMerge23$Clone_Sequence %in% patientMerge[all,]$merge)) 300 three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$Clone_Sequence %in% patientMerge[all,]$merge) & !(patient3$Clone_Sequence %in% patientMerge13[one_three,]$merge) & !(patient3$Clone_Sequence %in% patientMerge23[two_three,]$merge))
301 301
302 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x)) 302 read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x))
303 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y)) 303 read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y))
304 read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.z)) 304 read3Count = append(read3Count, sum(patient3[three,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.z))
305 res1 = append(res1, sum(one)) 305 res1 = append(res1, sum(one))
362 p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) 362 p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
363 } else { 363 } else {
364 p = ggplot(scatterplot_locus_data, aes(type, Frequency)) 364 p = ggplot(scatterplot_locus_data, aes(type, Frequency))
365 } 365 }
366 p = p + geom_point(aes(colour=type), position="jitter") 366 p = p + geom_point(aes(colour=type), position="jitter")
367 p = p + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex])) 367 p = p + xlab("In one or in multiple samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
368 } else { 368 } else {
369 p = ggplot(NULL, aes(x=c("In one", "In multiple"),y=0)) + geom_blank(NULL) + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex])) 369 p = ggplot(NULL, aes(x=c("In one", "In multiple"),y=0)) + geom_blank(NULL) + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
370 } 370 }
371 png(paste(label1, "_", label2, "_", label3, "_", onShort, "_", product[iter, titleIndex],"_scatter.png", sep="")) 371 png(paste(label1, "_", label2, "_", label3, "_", onShort, "_", product[iter, titleIndex],"_scatter.png", sep=""))
372 print(p) 372 print(p)