Mercurial > repos > davidvanzessen > phenotype_gene_relations
changeset 25:bce9fdf89e48 draft default tip
Uploaded
| author | davidvanzessen |
|---|---|
| date | Mon, 16 Nov 2015 07:12:40 -0500 |
| parents | 14afe3c8a3d5 |
| children | |
| files | phenotype_gene_relations_plot.r |
| diffstat | 1 files changed, 3 insertions(+), 5 deletions(-) [+] |
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--- a/phenotype_gene_relations_plot.r Mon Nov 16 07:06:56 2015 -0500 +++ b/phenotype_gene_relations_plot.r Mon Nov 16 07:12:40 2015 -0500 @@ -11,7 +11,7 @@ omt5=strsplit(args[6], ",")[[1]] inheritance=strsplit(args[7], ",")[[1]] orderby.list=as.character(args[8]) -orderby = ifelse(nchar(orderby) == 0, "1", orderby) +orderby.list = ifelse(orderby.list == "None", "1", orderby.list) outdir=args[9] dat = read.table(input, header=T, sep="\t", comment.char="#", quote = "") @@ -63,13 +63,11 @@ filter = dat.sub2$GROUP.CODE == as.numeric(orderby) & dat.sub2$ratio != 0 print(paste("orderby:",orderby, "+1:", sum(filter))) if(sum(filter) > 0){ - #dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + max(dat.sub2$ratio) - dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + 1 + dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + max(dat.sub2$ratio) } } -#dat.sub2[dat.sub2$disease.gene.order < max(dat.sub2$ratio),"disease.gene.order"] = 0 -dat.sub2[dat.sub2$disease.gene.order < 1,"disease.gene.order"] = 0 +dat.sub2[dat.sub2$disease.gene.order <= max(dat.sub2$ratio),"disease.gene.order"] = 0 print(paste("min ratio:", min(dat.sub2$ratio)))