Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

comparison RScript.r @ 61:77a090cd0e02 draft

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author davidvanzessen
date Fri, 30 Oct 2015 04:39:33 -0400
parents 28c3695259c1
children b1ad6f515338
comparison
equal deleted inserted replaced
60:28c3695259c1 61:77a090cd0e02
440 cat("<tr><td>Starting Frequency analysis</td></tr>", file=logfile, append=T) 440 cat("<tr><td>Starting Frequency analysis</td></tr>", file=logfile, append=T)
441 441
442 interval = intervalFreq 442 interval = intervalFreq
443 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval)) 443 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
444 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 444 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
445 lapply(patients[4], FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T) 445 lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="Frequency", appendtxt=T)
446 446
447 cat("<tr><td>Starting Cell Count analysis</td></tr>", file=logfile, append=T) 447 cat("<tr><td>Starting Cell Count analysis</td></tr>", file=logfile, append=T)
448 448
449 interval = intervalReads 449 interval = intervalReads
450 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval)) 450 intervalOrder = data.frame("interval"=paste(">", interval, sep=""), "intervalOrder"=1:length(interval))
451 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 451 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
452 lapply(patients[4], FUN=patientCountOnColumn, product = product, interval=interval, on="normalized_read_count") 452 lapply(patients, FUN=patientCountOnColumn, product = product, interval=interval, on="normalized_read_count")
453 453
454 if(nrow(single_patients) > 0){ 454 if(nrow(single_patients) > 0){
455 scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count)))) 455 scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
456 p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000)) 456 p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
457 p = p + geom_point(aes(colour=type), position="jitter") 457 p = p + geom_point(aes(colour=type), position="jitter")
969 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 969 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
970 970
971 one = triplets[triplets$Sample == "14696_reg_BM",] 971 one = triplets[triplets$Sample == "14696_reg_BM",]
972 two = triplets[triplets$Sample == "24536_reg_BM",] 972 two = triplets[triplets$Sample == "24536_reg_BM",]
973 three = triplets[triplets$Sample == "24062_reg_BM",] 973 three = triplets[triplets$Sample == "24062_reg_BM",]
974 #tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="normalized_read_count", T) 974 tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="normalized_read_count", T)
975 975
976 one = triplets[triplets$Sample == "16278_Left",] 976 one = triplets[triplets$Sample == "16278_Left",]
977 two = triplets[triplets$Sample == "26402_Left",] 977 two = triplets[triplets$Sample == "26402_Left",]
978 three = triplets[triplets$Sample == "26759_Left",] 978 three = triplets[triplets$Sample == "26759_Left",]
979 #tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="normalized_read_count", T) 979 tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="normalized_read_count", T)
980 980
981 one = triplets[triplets$Sample == "16278_Right",] 981 one = triplets[triplets$Sample == "16278_Right",]
982 two = triplets[triplets$Sample == "26402_Right",] 982 two = triplets[triplets$Sample == "26402_Right",]
983 three = triplets[triplets$Sample == "26759_Right",] 983 three = triplets[triplets$Sample == "26759_Right",]
984 tripletAnalysis(one, "16278_Right_Trio", two, "26402_Right_Trio", three, "26759_Right_Trio", product=product, interval=interval, on="normalized_read_count", T) 984 tripletAnalysis(one, "16278_Right_Trio", two, "26402_Right_Trio", three, "26759_Right_Trio", product=product, interval=interval, on="normalized_read_count", T)
990 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval))) 990 product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
991 991
992 one = triplets[triplets$Sample == "14696_reg_BM",] 992 one = triplets[triplets$Sample == "14696_reg_BM",]
993 two = triplets[triplets$Sample == "24536_reg_BM",] 993 two = triplets[triplets$Sample == "24536_reg_BM",]
994 three = triplets[triplets$Sample == "24062_reg_BM",] 994 three = triplets[triplets$Sample == "24062_reg_BM",]
995 #tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="Frequency", F) 995 tripletAnalysis(one, "14696_1_Trio", two, "14696_2_Trio", three, "14696_3_Trio", product=product, interval=interval, on="Frequency", F)
996 996
997 one = triplets[triplets$Sample == "16278_Left",] 997 one = triplets[triplets$Sample == "16278_Left",]
998 two = triplets[triplets$Sample == "26402_Left",] 998 two = triplets[triplets$Sample == "26402_Left",]
999 three = triplets[triplets$Sample == "26759_Left",] 999 three = triplets[triplets$Sample == "26759_Left",]
1000 #tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="Frequency", F) 1000 tripletAnalysis(one, "16278_Left_Trio", two, "26402_Left_Trio", three, "26759_Left_Trio", product=product, interval=interval, on="Frequency", F)
1001 1001
1002 one = triplets[triplets$Sample == "16278_Right",] 1002 one = triplets[triplets$Sample == "16278_Right",]
1003 two = triplets[triplets$Sample == "26402_Right",] 1003 two = triplets[triplets$Sample == "26402_Right",]
1004 three = triplets[triplets$Sample == "26759_Right",] 1004 three = triplets[triplets$Sample == "26759_Right",]
1005 tripletAnalysis(one, "16278_Right_Trio", two, "26402_Right_Trio", three, "26759_Right_Trio", product=product, interval=interval, on="Frequency", F) 1005 tripletAnalysis(one, "16278_Right_Trio", two, "26402_Right_Trio", three, "26759_Right_Trio", product=product, interval=interval, on="Frequency", F)