Mercurial > repos > davidvanzessen > clonal_sequences_in_paired_samples
changeset 27:dd8518ea23dd draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 25 Feb 2015 09:18:14 -0500 |
| parents | f35c127b29b1 |
| children | a63ccc36f5a4 |
| files | RScript.r |
| diffstat | 1 files changed, 14 insertions(+), 6 deletions(-) [+] |
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--- a/RScript.r Tue Feb 24 11:19:26 2015 -0500 +++ b/RScript.r Wed Feb 25 09:18:14 2015 -0500 @@ -268,7 +268,7 @@ scatterplot_data_columns = c("Clone_Sequence", "Frequency", "normalized_read_count", "V_Segment_Major_Gene", "J_Segment_Major_Gene") scatterplot_data = rbind(patient1[,scatterplot_data_columns], patient2[,scatterplot_data_columns], patient3[,scatterplot_data_columns]) scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$Clone_Sequence),] - scatterplot_data$type = factor(x="single", levels=c("In one", "In two", "In three")) + scatterplot_data$type = factor(x="In one", levels=c("In one", "In two", "In three", "In multiple")) res1 = vector() res2 = vector() @@ -349,11 +349,19 @@ } } else { #scatterplot data scatterplot_locus_data = scatterplot_data[grepl(V_Segment, scatterplot_data$V_Segment_Major_Gene) & grepl(J_Segment, scatterplot_data$J_Segment_Major_Gene),] - scatterplot_locus_data$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") - #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") - scatterplot_locus_data[(scatterplot_locus_data$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x),]$type = "In three" - scatterplot_locus_data$type = ifelse(scatterplot_locus_data$type == "In one", "In one", "In multiple") - + in_two = (scatterplot_locus_data$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,]$Clone_Sequence.x) + if(sum(in_two) > 0){ + scatterplot_locus_data[in_two,]$type = "In two" + } + in_three = (scatterplot_locus_data$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x) + if(sum(in_three)> 0){ + scatterplot_locus_data[in_three,]$type = "In three" + } + not_in_one = scatterplot_locus_data$type != "In one" + print(not_in_one) + if(sum(not_in_one) > 0){ + scatterplot_locus_data[not_in_one,]$type = "In multiple" + } p = NULL if(nrow(scatterplot_locus_data) != 0){ if(on == "normalized_read_count"){