# HG changeset patch
# User artbio
# Date 1604169280 0
# Node ID 3351ca630a012dcf773ce499efad71d717471899
# Parent  e08419b8ec2407577fc666ef1ed47a06d38ebd2f
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit b2f58ce7826f8d9fe5524a6f2c5688ac816bb559"

diff -r e08419b8ec24 -r 3351ca630a01 signature_score.R
--- a/signature_score.R	Tue Jul 09 10:52:29 2019 -0400
+++ b/signature_score.R	Sat Oct 31 18:34:40 2020 +0000
@@ -118,7 +118,7 @@
 write.table(signature.covariances, file=opt$covariances, quote=F, row.names=F, sep="\t")
 
 # compute signature.correlations
-signature.correlations <- as.data.frame(cov(t(signature.counts)))
+signature.correlations <- as.data.frame(cor(t(signature.counts)))
 signature.correlations <- cbind(gene=rownames(signature.correlations), signature.correlations)
 write.table(signature.correlations, file=opt$correlations, quote=F, row.names=F, sep="\t")
 
@@ -221,4 +221,4 @@
   quote = F,
   col.names = T,
   row.names = F
-)
\ No newline at end of file
+)
diff -r e08419b8ec24 -r 3351ca630a01 signature_score.xml
--- a/signature_score.xml	Tue Jul 09 10:52:29 2019 -0400
+++ b/signature_score.xml	Sat Oct 31 18:34:40 2020 +0000
@@ -88,6 +88,14 @@
 * the number of genes detected in the cell/library
 * the total number of aligned reads in the cell/library
 
+And also several tables or PDF : 
+
+* signature genes covariance matrix
+* signature genes correlation matrix
+* genes statistics (mean expression, standard deviation, variance, percentage of detection)
+* a pdf with the violin plot of signature score for each transcriptomes splitted by their category (HIGH/LOW)
+
+
     </help>
     <citations>
         <citation type="bibtex">
diff -r e08419b8ec24 -r 3351ca630a01 test-data/correlations.tsv
--- a/test-data/correlations.tsv	Tue Jul 09 10:52:29 2019 -0400
+++ b/test-data/correlations.tsv	Sat Oct 31 18:34:40 2020 +0000
@@ -1,6 +1,6 @@
 gene	ZNF454	ACAD9	LAIR1	GAPDH	CHTOP
-ZNF454	11.9837926366092	1.26124926841842	-4.79209750033634	1.28119046792732	4.7040467133562
-ACAD9	1.26124926841842	36.4037213995154	0.987902621359844	1.57734537259074	3.12155500211722
-LAIR1	-4.79209750033634	0.987902621359844	58.8639861631431	-0.564659931985148	1.20262555258428
-GAPDH	1.28119046792732	1.57734537259074	-0.564659931985148	24.8789307434615	0.808639324069219
-CHTOP	4.7040467133562	3.12155500211722	1.20262555258428	0.808639324069219	44.8667386237237
+ZNF454	1	0.0603852534621041	-0.18042788931775	0.0741994524610916	0.202867385523867
+ACAD9	0.0603852534621041	1	0.0213410809230789	0.0524128830600715	0.0772388590342458
+LAIR1	-0.18042788931775	0.0213410809230789	1	-0.0147552401307713	0.0234014809388211
+GAPDH	0.0741994524610916	0.0524128830600715	-0.0147552401307713	1	0.0242034207612757
+CHTOP	0.202867385523867	0.0772388590342458	0.0234014809388211	0.0242034207612757	1