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Commit 8a0787f6 authored by Aurelien Brionne's avatar Aurelien Brionne
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correct showIC=FALSE arg in GOterms_heatmap method

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Package: ViSEAGO
Version: 1.3.15
Version: 1.3.16
Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
Author: Aurelien Brionne [aut, cre],
Amelie Juanchich [aut],
......
......@@ -73,7 +73,7 @@ CHANGES IN VERSION 1.3
o upset print update
o merge_enrich_terms upgrade pvalue cutoff
o merge_enrich_terms globale upgrade
o GOterms_heatmap remove row side colors text
o GOterms_heatmap remove row side colors text and correct showIC column
o vignettes update
o annotate() update for uniprot
o fgsea support
......
......@@ -987,7 +987,9 @@ setMethod(
}
# remove row side colors text mention
hm$x$layout$annotations[[1]]$text<-""
if(length(hm$x$layout$annotations)>0){
hm$x$layout$annotations[[1]]$text<-""
}
# hm to list
hm<-list(hm)
......
......@@ -20,7 +20,7 @@
#' Defaults fgseaMultilevel parameters were used for perform test
#' except the \code{eps} arg that was set to 0 for better pvalues estimation.\cr
#' A gene frequency (\%) of leadingEdge/size is added to output \code{data.table}.
#' @return a \code{\link[fgsea]{fgsea-class}} object.
#' @return a \code{\link{fgsea-class}} object.
#' @references
#' Korotkevich G, Sukhov V, Sergushichev A (2019). "Fast gene set enrichment analysis." bioRxiv. doi: 10.1101/060012, http://biorxiv.org/content/early/2016/06/20/060012.
#' @include fgsea.R
......
......@@ -27,7 +27,7 @@ remotes::install_gitlab(
devtools::build("ViSEAGO")
# install package (from R console)
install.packages("ViSEAGO_1.3.15.tar.gz", repos = NULL, type = "source")
install.packages("ViSEAGO_1.3.16.tar.gz", repos = NULL, type = "source")
```
## Citation
......
......@@ -37,7 +37,7 @@ runfgsea(
\item{params}{a \code{list} with \code{\link[fgsea]{fgseaSimple}} or \code{\link[fgsea]{fgseaMultilevel}} parameters.}
}
\value{
a \code{\link[fgsea]{fgsea-class}} object.
a \code{\link{fgsea-class}} object.
}
\description{
This method perform fast gene set enrichment analysis (GSEA) using \pkg{fgsea} package.
......
......@@ -466,7 +466,7 @@ Enriched GO terms are ranked in a dendrogram and colored depending on their clus
# Create GOterms heatmap
Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs,
showIC=TRUE,
showIC=FALSE,
showGOlabels =FALSE,
GO.tree=list(
tree=list(
......
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