Mercurial > repos > iuc > goseq
changeset 5:bbcf5f7f2af2 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/goseq commit 2dffcdff171ebf695ef0fc7eb8f8264f0d132115
| author | iuc |
|---|---|
| date | Mon, 28 Jan 2019 04:27:40 -0500 |
| parents | ae39895af5fe |
| children | 07f6832bdd4d |
| files | goseq.r goseq.xml |
| diffstat | 2 files changed, 13 insertions(+), 13 deletions(-) [+] |
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--- a/goseq.r Sun Sep 30 09:27:05 2018 -0400 +++ b/goseq.r Mon Jan 28 04:27:40 2019 -0500 @@ -134,7 +134,7 @@ sink(zz) GO.samp=goseq(pwf, genome = genome, id = gene_id, method="Sampling", repcnt=repcnt, use_genes_without_cat = use_genes_without_cat, gene2cat=go_map) sink() - + GO.samp$p.adjust.over_represented = p.adjust(GO.samp$over_represented_pvalue, method=p_adj_method) GO.samp$p.adjust.under_represented = p.adjust(GO.samp$under_represented_pvalue, method=p_adj_method) write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) @@ -156,15 +156,15 @@ pdf("top10.pdf") for (m in names(results)) { p <- results[[m]] %>% - top_n(10, wt=-p.adjust.over_represented) %>% + top_n(10, wt=-over_represented_pvalue) %>% mutate(hitsPerc=numDEInCat*100/numInCat) %>% ggplot(aes(x=hitsPerc, y=substr(term, 1, 40), # only use 1st 40 chars of terms otherwise squashes plot - colour=p.adjust.over_represented, + colour=over_represented_pvalue, size=numDEInCat)) + geom_point() + expand_limits(x=0) + - labs(x="% DE in category", y="Category", colour="adj. P value", size="Count", title=paste("Top over-represented categories in", cats_title), subtitle=paste(m, " method")) + + labs(x="% DE in category", y="Category", colour="P value", size="Count", title=paste("Top over-represented categories in", cats_title), subtitle=paste(m, " method")) + theme(plot.title = element_text(hjust = 0.5), plot.subtitle = element_text(hjust = 0.5)) print(p) }
--- a/goseq.xml Sun Sep 30 09:27:05 2018 -0400 +++ b/goseq.xml Mon Jan 28 04:27:40 2019 -0500 @@ -1,14 +1,14 @@ -<tool id="goseq" name="goseq" version="1.30.1"> +<tool id="goseq" name="goseq" version="1.32.0"> <description>tests for overrepresented gene categories</description> <requirements> + <requirement type="package" version="1.32.0">bioconductor-goseq</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.hs.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.dm.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.dr.eg.db</requirement> + <requirement type="package" version="3.6.0">bioconductor-org.mm.eg.db</requirement> + <requirement type="package" version="0.7.8">r-dplyr</requirement> + <requirement type="package" version="3.1.0">r-ggplot2</requirement> <requirement type="package" version="1.6.0">r-optparse</requirement> - <requirement type="package" version="1.30.0">bioconductor-goseq</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.hs.eg.db</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.dm.eg.db</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.dr.eg.db</requirement> - <requirement type="package" version="3.5.0">bioconductor-org.mm.eg.db</requirement> - <requirement type="package" version="0.7.6">r-dplyr</requirement> - <requirement type="package" version="3.0.0">r-ggplot2</requirement> </requirements> <stdio> <regex match="Execution halted" @@ -203,7 +203,7 @@ <output name="wallenius_tab"> <assert_contents> <has_text_matching expression="category.*over_represented_pvalue.*under_represented_pvalue.*numDEInCat.*numInCat.*term.*ontology.*p.adjust.over_represented.*p.adjust.under_represented" /> - <has_text_matching expression="GO:0031324.*0.08" /> + <has_text_matching expression="GO:0031324.*0.12" /> </assert_contents> </output> </test>