Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

diff RScript.r @ 25:99020e5ce46c draft

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author davidvanzessen
date Tue, 24 Feb 2015 10:10:45 -0500
parents 6904186d13b9
children f35c127b29b1
line wrap: on
line diff
--- a/RScript.r	Tue Feb 24 09:12:28 2015 -0500
+++ b/RScript.r	Tue Feb 24 10:10:45 2015 -0500
@@ -291,13 +291,13 @@
     #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) 
     all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge$thresholdValue > threshhold)
     
-    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,]$merge))
-    one_three = (grepl(V_Segment, patientMerge13$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge13$J_Segment_Major_Gene.x) & patientMerge13$thresholdValue > threshhold & !(patientMerge13$Clone_Sequence %in% patientMerge[all,]$merge))
-    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,]$merge))
+    one_two = (grepl(V_Segment, patientMerge12$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))
+    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,]$merge))
+    two_three = (grepl(V_Segment, patientMerge23$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))
     
-    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))
-    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))
-    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))
+    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))
+    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))
+    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))
     
     read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x))
     read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y))
@@ -364,7 +364,7 @@
           p = ggplot(scatterplot_locus_data, aes(type, Frequency)) 
         }
         p = p + geom_point(aes(colour=type), position="jitter")
-        p = p + xlab("In two or in three of the samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
+        p = p + xlab("In one or in multiple samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))
       } else {
         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]))
       }