Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples

changeset 70:9643b1fd9c45 draft default tip

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Uploaded
author davidvanzessen
date Thu, 26 May 2016 09:37:48 -0400
parents c532b3f8dc97
children
files RScript.r
diffstat 1 files changed, 7 insertions(+), 4 deletions(-) [+]
line wrap: on
line diff
--- a/RScript.r	Wed Jan 06 11:00:00 2016 -0500
+++ b/RScript.r	Thu May 26 09:37:48 2016 -0400
@@ -406,7 +406,10 @@
       if(nrow(scatterplot_locus_data) != 0){
         if(on == "normalized_read_count"){
           scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
-          p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), normalized_read_count, group=link)) + geom_line() + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,10^6)) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
+          #p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), normalized_read_count, group=link)) + geom_line() + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,10^6)) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
+          print(paste("scatterplot_locus_data:"))
+          print(head(scatterplot_locus_data))
+          p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), normalized_read_count, group=link)) + geom_line() + scale_y_log10(breaks=scales,labels=scales, limits=c(0,10^6)) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
         } else {
           p = ggplot(scatterplot_locus_data, aes(factor(reorder(type, type.order)), Frequency, group=link)) + geom_line() + scale_y_log10(limits=c(0.0001,100), breaks=c(0.0001, 0.001, 0.01, 0.1, 1, 10, 100), labels=c("0.0001", "0.001", "0.01", "0.1", "1", "10", "100")) + scale_x_discrete(breaks=levels(scatterplot_data$type), labels=levels(scatterplot_data$type), drop=FALSE)
         }
@@ -918,12 +921,12 @@
       }
       not_in_one = scatterplot_locus_data$type != "In one"
       if(sum(not_in_one) > 0){
-				scatterplot_locus_data[not_in_one,]$type = "In multiple"
+				#scatterplot_locus_data[not_in_one,]$type = "In multiple"
       }
       p = NULL
       if(nrow(scatterplot_locus_data) != 0){
         if(on == "normalized_read_count"){
-					scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
+		  scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
           p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
         } else {
           p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_log10(limits=c(0.0001,100), breaks=c(0.0001, 0.001, 0.01, 0.1, 1, 10, 100), labels=c("0.0001", "0.001", "0.01", "0.1", "1", "10", "100")) + expand_limits(y=c(0,100))
@@ -991,7 +994,7 @@
   dev.off()
 }
 
-if(F & nrow(triplets) != 0){
+if(nrow(triplets) != 0){
 
   cat("<tr><td>Starting triplet analysis</td></tr>", file=logfile, append=T)