# HG changeset patch
# User davidvanzessen
# Date 1441291679 14400
# Node ID 98a908a5cd2fef276fbe8f2692cf0a8a151ac705
# Parent 38f0e68d1bac2c5df45025987396a8ed57808e26
Uploaded
diff -r 38f0e68d1bac -r 98a908a5cd2f OMT_coding.txt
diff -r 38f0e68d1bac -r 98a908a5cd2f phenotype_gene_relations_plot.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phenotype_gene_relations_plot.r Thu Sep 03 10:47:59 2015 -0400
@@ -0,0 +1,94 @@
+library(reshape2)
+library(ggplot2)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+input=args[1]
+omt1=strsplit(args[2], ",")[[1]]
+omt2=strsplit(args[3], ",")[[1]]
+omt3=strsplit(args[4], ",")[[1]]
+omt4=strsplit(args[5], ",")[[1]]
+omt5=strsplit(args[6], ",")[[1]]
+inheritance=strsplit(args[7], ",")[[1]]
+outdir=args[8]
+
+dat = read.table(input, header=T, sep="\t", comment.char="#", quote = "")
+
+setwd(outdir)
+
+dat$disease.gene = paste(dat$diseaseId, dat$gene.symbol)
+
+OMTs = dat$OMT.1 %in% omt1 | dat$OMT.2 %in% omt2 | dat$OMT.3 %in% omt3 | dat$OMT.4 %in% omt4 | dat$OMT.5 %in% omt5
+
+dat.sub = dat[OMTs,]
+
+selectA = dcast(dat.sub, OMT.5~disease.gene, length, value.var="disease.gene")
+
+selectA[selectA > 0] = 1
+
+selectA = selectA[,colSums(selectA) == nrow(selectA)]
+
+disease.in.omt = dat$disease.gene %in% names(selectA)
+inheritance.filter = dat$inheritance %in% inheritance
+
+dat.sub2 = dat[OMTs & disease.in.omt & inheritance.filter ,c("disease.gene", "GROUP.CODE", "ratio")]
+
+dat.sub2 = dat.sub2[!duplicated(dat.sub2),]
+
+p = ggplot(dat.sub2, aes(disease.gene, GROUP.CODE)) + geom_tile(aes(fill = ratio), colour = "white") + scale_fill_gradient(low = "white",high = "red")
+
+p = p + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+
+png("plot1.png")
+print(p)
+dev.off()
+
+dat.sub3 = dat[OMTs & disease.in.omt & inheritance.filter, c("diseaseId", "HPO.term.name")]
+dat.sub3$value = 1
+p = ggplot(dat.sub3, aes(diseaseId, HPO.term.name)) + geom_tile(aes(fill = value), colour = "white") + scale_fill_gradient(low = "red",high = "red")
+
+p = p + theme(axis.text.x = element_text(angle = 45, hjust = 1))
+
+png("plot2.png")
+print(p)
+dev.off()
+
+dat.sub4 = dat[disease.in.omt & dat$diseaseId %in% dat.sub3$diseaseId, c("diseaseId", "OMT.5.name")]
+dat.sub4$value = 1
+p = ggplot(dat.sub4, aes(diseaseId, OMT.5.name)) + geom_tile(aes(fill = value), colour = "white") + scale_fill_gradient(low = "red",high = "red")
+
+p = p + theme(axis.text.x = element_text(angle = 45, hjust = 1))
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+png("plot3.png", width=length(unique(dat.sub3$diseaseId)) * 30 + 200)
+print(p)
+dev.off()
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diff -r 38f0e68d1bac -r 98a908a5cd2f phenotype_gene_relations_plot.sh
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phenotype_gene_relations_plot.sh Thu Sep 03 10:47:59 2015 -0400
@@ -0,0 +1,33 @@
+set -e
+
+dir="$(cd "$(dirname "$0")" && pwd)"
+
+input="$1"
+omt1="$2"
+omt2="$3"
+omt3="$4"
+omt4="$5"
+omt5="$6"
+inheritance="$7"
+outdir="$8"
+html="$9"
+
+echo "input: ${input}"
+echo "omt1: ${omt1}"
+echo "omt2: ${omt2}"
+echo "omt3: ${omt3}"
+echo "omt4: ${omt4}"
+echo "omt5: ${omt5}"
+echo "inheritance: ${inheritance}"
+echo "html: ${html}"
+echo "outdir: ${outdir}"
+
+mkdir "$outdir"
+
+
+
+Rscript --verbose $dir/phenotype_gene_relations_plot.r "$input" "$omt1" "$omt2" "$omt3" "$omt4" "$omt5" "$inheritance" "$outdir" 2>&1
+
+echo "
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+echo "
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+echo "
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diff -r 38f0e68d1bac -r 98a908a5cd2f phenotype_gene_relations_plot.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/phenotype_gene_relations_plot.xml Thu Sep 03 10:47:59 2015 -0400
@@ -0,0 +1,157 @@
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+ phenotype_gene_relations_plot.sh $input "$omt1" "$omt2" "$omt3" "$omt4" "$omt5" "$inheritance" $output.files_path $output
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