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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 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 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
Author: Aurelien Brionne [aut, cre], Author: Aurelien Brionne [aut, cre],
Amelie Juanchich [aut], Amelie Juanchich [aut],
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...@@ -73,7 +73,7 @@ CHANGES IN VERSION 1.3 ...@@ -73,7 +73,7 @@ CHANGES IN VERSION 1.3
o upset print update o upset print update
o merge_enrich_terms upgrade pvalue cutoff o merge_enrich_terms upgrade pvalue cutoff
o merge_enrich_terms globale upgrade 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 vignettes update
o annotate() update for uniprot o annotate() update for uniprot
o fgsea support o fgsea support
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...@@ -987,7 +987,9 @@ setMethod( ...@@ -987,7 +987,9 @@ setMethod(
} }
# remove row side colors text mention # 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 to list
hm<-list(hm) hm<-list(hm)
......
...@@ -20,7 +20,7 @@ ...@@ -20,7 +20,7 @@
#' Defaults fgseaMultilevel parameters were used for perform test #' Defaults fgseaMultilevel parameters were used for perform test
#' except the \code{eps} arg that was set to 0 for better pvalues estimation.\cr #' 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}. #' 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 #' @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. #' 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 #' @include fgsea.R
......
...@@ -27,7 +27,7 @@ remotes::install_gitlab( ...@@ -27,7 +27,7 @@ remotes::install_gitlab(
devtools::build("ViSEAGO") devtools::build("ViSEAGO")
# install package (from R console) # 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 ## Citation
......
...@@ -37,7 +37,7 @@ runfgsea( ...@@ -37,7 +37,7 @@ runfgsea(
\item{params}{a \code{list} with \code{\link[fgsea]{fgseaSimple}} or \code{\link[fgsea]{fgseaMultilevel}} parameters.} \item{params}{a \code{list} with \code{\link[fgsea]{fgseaSimple}} or \code{\link[fgsea]{fgseaMultilevel}} parameters.}
} }
\value{ \value{
a \code{\link[fgsea]{fgsea-class}} object. a \code{\link{fgsea-class}} object.
} }
\description{ \description{
This method perform fast gene set enrichment analysis (GSEA) using \pkg{fgsea} package. 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 ...@@ -466,7 +466,7 @@ Enriched GO terms are ranked in a dendrogram and colored depending on their clus
# Create GOterms heatmap # Create GOterms heatmap
Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap( Wang_clusters_wardD2<-ViSEAGO::GOterms_heatmap(
myGOs, myGOs,
showIC=TRUE, showIC=FALSE,
showGOlabels =FALSE, showGOlabels =FALSE,
GO.tree=list( GO.tree=list(
tree=list( tree=list(
......
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