Mercurial > repos > artbio > gsc_signature_score
changeset 3:3351ca630a01 draft
"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/gsc_signature_score commit b2f58ce7826f8d9fe5524a6f2c5688ac816bb559"
| author | artbio |
|---|---|
| date | Sat, 31 Oct 2020 18:34:40 +0000 |
| parents | e08419b8ec24 |
| children | 31da579595c5 |
| files | signature_score.R signature_score.xml test-data/correlations.tsv |
| diffstat | 3 files changed, 15 insertions(+), 7 deletions(-) [+] |
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--- 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 +)
--- 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">
--- 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