Mercurial > repos > davidvanzessen > phenotype_gene_relations
changeset 23:0fa1b346ab52 draft
Uploaded
| author | davidvanzessen |
|---|---|
| date | Wed, 11 Nov 2015 08:36:42 -0500 |
| parents | 04d8e7add1ba |
| children | 14afe3c8a3d5 |
| files | phenotype_gene_relations_plot.r phenotype_gene_relations_plot.sh |
| diffstat | 2 files changed, 7 insertions(+), 1 deletions(-) [+] |
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--- a/phenotype_gene_relations_plot.r Tue Nov 10 10:04:46 2015 -0500 +++ b/phenotype_gene_relations_plot.r Wed Nov 11 08:36:42 2015 -0500 @@ -85,6 +85,7 @@ png("plot1.png", width=length(unique(dat.sub2$disease.gene)) * 30 + 300) print(p) dev.off() +write.table(dat.sub2, "plot1.txt", quote=F, sep="\t", row.names=F, col.names=T) dat.sub3 = dat[OMTs & disease.in.omt & inheritance.filter, c("diseaseId", "HPO.term.name")] dat.sub3$value = 1 @@ -95,6 +96,7 @@ png("plot2.png", width=length(unique(dat.sub3$diseaseId)) * 20 + 300) print(p) dev.off() +write.table(dat.sub3, "plot2.txt", quote=F, sep="\t", row.names=F, col.names=T) dat.sub4 = dat[disease.in.omt & dat$diseaseId %in% dat.sub3$diseaseId, c("diseaseId", "OMT.5.name")] dat.sub4 = dat.sub4[!duplicated(dat.sub4),] @@ -109,11 +111,12 @@ png("plot3.png", width=length(unique(dat.sub3$diseaseId)) * 20 + 300) print(p) dev.off() +write.table(dat.sub4, "plot3.txt", quote=F, sep="\t", row.names=F, col.names=T) #order the table the same as the first plot x axis disease.gene.url = dat[OMTs & disease.in.omt & inheritance.filter ,c("disease.gene", "diseaseId", "gene.symbol", "url")] disease.gene.url = disease.gene.url[!duplicated(disease.gene.url),] -disease.gene.url = merge(disease.gene.url, dat.sub2[,c("disease.gene", "disease.gene.order")], by="disease.gene") +disease.gene.url = merge(disease.gene.url, dat.sub2[!duplicated(dat.sub2$disease.gene),c("disease.gene", "disease.gene.order")], by="disease.gene", all.x=T) disease.gene.url = disease.gene.url[order(-disease.gene.url$disease.gene.order),] disease.gene.url = disease.gene.url[,c("diseaseId", "gene.symbol", "url")]
--- a/phenotype_gene_relations_plot.sh Tue Nov 10 10:04:46 2015 -0500 +++ b/phenotype_gene_relations_plot.sh Wed Nov 11 08:36:42 2015 -0500 @@ -35,9 +35,12 @@ echo "<div style='width: 10000px;'>" >> "$html" echo "<img src='plot1_avg.png' /><br />" >> "$html" echo "<img src='plot1.png' /><br />" >> "$html" +echo "<a href='plot1.txt'>Download</a><br />" >> "$html" echo "</div>" >> "$html" echo "<img src='plot2.png' /><br />" >> "$html" +echo "<a href='plot2.txt'>Download</a><br />" >> "$html" echo "<img src='plot3.png' /><br />" >> "$html" +echo "<a href='plot3.txt'>Download</a><br />" >> "$html" echo "<table border='1'>" >> $html first="true"