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changeset 9:98a908a5cd2f draft

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Uploaded
author davidvanzessen
date Thu, 03 Sep 2015 10:47:59 -0400
parents 38f0e68d1bac
children 768df9ba57e8
files OMT_coding.txt phenotype_gene_relations_plot.r phenotype_gene_relations_plot.sh phenotype_gene_relations_plot.xml
diffstat 3 files changed, 284 insertions(+), 0 deletions(-) [+]
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--- /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))
+
+png("plot3.png", width=length(unique(dat.sub3$diseaseId)) * 30 + 200)
+print(p)
+dev.off()
+
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phenotype_gene_relations_plot.sh	Thu Sep 03 10:47:59 2015 -0400
@@ -0,0 +1,33 @@
+set -e
+
+dir="$(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" "$outdir" 2>&1
+
+echo "<img src='plot1.png' /><br />" >> "$html"
+echo "<img src='plot2.png' /><br />" >> "$html"
+echo "<img src='plot3.png' /><br />" >> "$html"
--- /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 @@
+<tool id="phenotype_gene_relations_plot" name="Phenotype Gene Relations plotting" version="1.0">
+	<description> </description>
+	<command interpreter="bash">
+		phenotype_gene_relations_plot.sh $input "$omt1" "$omt2" "$omt3" "$omt4" "$omt5" "$inheritance" $output.files_path $output
+	</command>
+	<inputs>
+        <param name="input" format="tabular" type="data" label="Input" />
+        <param name="omt1" format="tabular" type="select" multiple="true" label="OMT.1">
+					<option value="0">0 N/C</option>
+					<option value="1">1 1. Malformation</option>
+					<option value="2">2 2. Deformation</option>
+					<option value="3">3 3. Dysplasia</option>
+				</param>
+				<param name="omt2" format="tabular" type="select" multiple="true" label="OMT.2">
+					<option value="0">0 N/C</option>
+					<option value="11">11 1A. Entire limb malformations</option>
+					<option value="12">12 1B. Handplate malformations</option>
+					<option value="21">21 Constriction ring sequence</option>
+					<option value="22">22 Trigger digits</option>
+					<option value="31">31 3A. Hypertrophy</option>
+					<option value="32">32 3B. Tumorous conditions</option>
+				</param>
+				<param name="omt3" format="tabular" type="select" multiple="true" label="OMT.3">
+					<option value="0">0 N/C</option>
+						<option value="110">110 1A. NOS entire limb malformation</option>
+						<option value="111">111 1A1. Proximal-distal axis (entire limb)</option>
+						<option value="112">112 1A2. Radio-ulnar axis (entire limb)</option>
+						<option value="113">113 1A4. Unspecified axis (entire limb)</option>
+						<option value="114">114 1A3. Dorso-ventral axis (entire limb)</option>
+						<option value="120">120 1B. NOS handplate malformation</option>
+						<option value="121">121 1B1. Proximal-distal axis (hand)</option>
+						<option value="122">122 1B2. Radio-ulnar axis (hand)</option>
+						<option value="123">123 1B3. Dorso-ventral axis (hand)</option>
+						<option value="124">124 1B4. Unspecified axis (hand)</option>
+						<option value="210">210 Constriction ring sequence</option>
+						<option value="220">220 Trigger digits</option>
+						<option value="311">311 3A1. Whole limb hypertrophy</option>
+						<option value="312">312 3A2. Partial Limb hypertrophy</option>
+						<option value="321">321 3B1. Vascular tumors</option>
+						<option value="324">324 3B4. Skeletal tumors</option>
+				</param>
+				<param name="omt4" format="tabular" type="select" multiple="true" label="OMT.4">
+					<option value="0">0 N/C</option>
+					<option value="1100">1100 1A. NOS malformation (entire limb)</option>
+					<option value="1110">1110 1A1. NOS prox-distal axis (entire limb)</option>
+					<option value="1111">1111 1A1i. Brachymelia</option>
+					<option value="1112">1112 1A1ii. Symbrachydactyly</option>
+					<option value="1113">1113 1A1iii. Transverse deficiency</option>
+					<option value="1114">1114 1A1iv. Intersegmental deficiency</option>
+					<option value="1115">1115 1A1v. Limb duplication</option>
+					<option value="1120">1120 1A2. NOS rad-uln axis (entire limb)</option>
+					<option value="1121">1121 1A2i. Radial longitudinal deficiency</option>
+					<option value="1122">1122 1A2ii. Ulnar longitudinal deficiency</option>
+					<option value="1124">1124 1A2iv. Radioulnar synostosis</option>
+					<option value="1125">1125 1A2v. Congenital radial head dislocation</option>
+					<option value="1126">1126 1A2vi. Humeroradial synostosis</option>
+					<option value="1127">1127 1A2vii. Madelung deformity</option>
+					<option value="1132">1132 1A3ii. Ventral dimelia </option>
+					<option value="1141">1141 1A4i. Abberant shoulder (incl Sprengel deformity)</option>
+					<option value="1142">1142 1A4ii. Arthrogryposis</option>
+					<option value="1200">1200 1B. NOS malformation (hand)</option>
+					<option value="1211">1211 1B1i. Brachydactyly</option>
+					<option value="1213">1213 1B1iii. Transverse deficiency (no arm involvement)</option>
+					<option value="1220">1220 1B2. NOS rad-uln axis malformation (hand)</option>
+					<option value="1221">1221 1B2i. Radial deficiency of the hand</option>
+					<option value="1222">1222 1B2ii. Ulnar deficiency of the hand</option>
+					<option value="1223">1223 1B2iii. Radial polydactyly</option>
+					<option value="1224">1224 1B2iv. Triphalangeal thumb</option>
+					<option value="1225">1225 1B2v. Ulnar dimelia</option>
+					<option value="1232">1232 1B3ii. Ventral dimelia (incl hypoplastic/aplastic nail)</option>
+					<option value="1241">1241 1B4i. Softi tissue malformations</option>
+					<option value="1242">1242 1B4ii. Sekeltal deficiencies</option>
+					<option value="1243">1243 1B4iii. Complex anomalies of unspecified axis (hand)</option>
+					<option value="2100">2100 Constriction ring sequence</option>
+					<option value="2200">2200 Trigger digits</option>
+					<option value="3111">3111 3A1i. Hemihypertrophy</option>
+					<option value="3121">3121 3A2i. Macrodactyly</option>
+					<option value="3211">3211 3B1i. Hemangioma</option>
+					<option value="3212">3212 3B1ii. Vascular malformation</option>
+					<option value="3241">3241 3B4i. Osteochondromatosis</option>
+					<option value="3242">3242 3B4ii. Echondromatosis</option>
+					<option value="3244">3244 3B4iv. Epiphyseal abnormalities</option>
+				</param>
+				<param name="omt5" format="tabular" type="select" multiple="true" label="OMT.5">
+					<option value="0">0 N/C</option>
+						<option value="11000">11000 1A. NOS entire limb malformation</option>
+						<option value="11100">11100 1A1. NOS proximal-distal axis malformation</option>
+						<option value="11110">11110 1A1i. Brachymelia</option>
+						<option value="11121">11121 1A1iia. Poland Syndrome</option>
+						<option value="11130">11130 1A1iii. Transverse deficiency</option>
+						<option value="11140">11140 1A1iv. Intersegmental deficiency</option>
+						<option value="11150">11150 1A1v. Limb duplication</option>
+						<option value="11200">11200 1A2. NOS rad-uln axis (entire limb)</option>
+						<option value="11210">11210 1A2i. Radial longitudinal deficiency</option>
+						<option value="11220">11220 1A2ii. Ulnar longitudinal deficiency</option>
+						<option value="11240">11240 1A2iv. Radioulnar synostosis</option>
+						<option value="11250">11250 1A2v. Congenital radial head dislocation</option>
+						<option value="11260">11260 1A2vi. Humeroradial synostosis</option>
+						<option value="11270">11270 1A2vii. Madelung deformity</option>
+						<option value="11320">11320 1A3ii. Ventral dimelia </option>
+						<option value="11411">11411 1A4ia. Sprengel deformity</option>
+						<option value="11412">11412 1A4ib. Abnormal shoulder muscles</option>
+						<option value="11413">11413 1A4ic. NOS shoulder malformation</option>
+						<option value="11420">11420 1A4ii. Arthrogryposis</option>
+						<option value="12000">12000 1B. NOS handplate malformation</option>
+						<option value="12110">12110 1B1i. Brachydactyly</option>
+						<option value="12130">12130 1B1iii. Transverse deficiency (no arm involvement)</option>
+						<option value="12200">12200 1B2. NOS rad-uln axis malformation (hand)</option>
+						<option value="12210">12210 1B2i. Radial deficiency of the hand</option>
+						<option value="12220">12220 1B2ii. Ulnar deficiency of the hand</option>
+						<option value="12230">12230 1B2iii. Radial polydactyly</option>
+						<option value="12240">12240 1B2iv. Triphalangeal thumb</option>
+						<option value="12250">12250 1B2v. Ulnar dimelia</option>
+						<option value="12320">12320 1B3ii. Ventral dimelia (incl hypoplastic/aplastic nail)</option>
+						<option value="12411">12411 1B4ia. Syndactyly</option>
+						<option value="12412">12412 1B4ib. Camptodactyly</option>
+						<option value="12413">12413 1B4ic. Thumb in palm deformity</option>
+						<option value="12414">12414 1B4id. Distal arthrogryposis</option>
+						<option value="12421">12421 1B4iia. Clinodactyly</option>
+						<option value="12423">12423 1B4iib. Synostosis/symphalangism</option>
+						<option value="12431">12431 1B4iiia. Complex syndactyly</option>
+						<option value="12432">12432 1B4iiib. Synpolydactyly</option>
+						<option value="12434">12434 1B4iiid. Apert Hand</option>
+						<option value="21000">21000 Constriction ring sequence</option>
+						<option value="22000">22000 Trigger digits</option>
+						<option value="31110">31110 3A1i. Hemihypertrophy</option>
+						<option value="31210">31210 3A2i. Macrodactyly</option>
+						<option value="32110">32110 3B1i. Hemangioma</option>
+						<option value="32120">32120 3B1ii. Vascular malformation</option>
+						<option value="32410">32410 3B4i. Osteochondromatosis</option>
+						<option value="32420">32420 3B4ii. Echondromatosis</option>
+						<option value="32440">32440 3B4iv. Epiphyseal abnormalities</option>
+				</param>
+        <param name="inheritance" format="tabular" type="select" multiple="true" label="Inheritance">
+					<option value="unique.final.inheritance.">unique.final.inheritance.</option>
+					<option value="No inheritance pattern available">No inheritance pattern available</option>
+					<option value="Autosomal dominant inheritance">Autosomal dominant inheritance</option>
+					<option value="X-linked dominant inheritance">X-linked dominant inheritance</option>
+					<option value="Autosomal recessive inheritance">Autosomal recessive inheritance</option>
+					<option value="X-linked recessive inheritance">X-linked recessive inheritance</option>
+					<option value="X-linked inheritance">X-linked inheritance</option>
+					<option value="Somatic mosaicism">Somatic mosaicism</option>
+					<option value="Mitochondrial inheritance">Mitochondrial inheritance</option>
+					<option value="Somatic mutation">Somatic mutation</option>
+					<option value="Autosomal dominant contiguous gene syndrome">Autosomal dominant contiguous gene syndrome</option>
+					<option value="Sex-limited autosomal dominant">Sex-limited autosomal dominant</option>
+				</param>
+	</inputs>
+	<outputs>
+		<data format="html" name="output" label="Phenotype Gene Rel plotting on: ${input.name} "/>
+	</outputs>
+	<help>
+stuff, words, things
+
+	</help>
+
+</tool>