diff --git a/DESCRIPTION b/DESCRIPTION index 4decac6c2673e72c7f13a9c99ece79b362cfc610..bfdfcbbb914e5be6ff5c48e58c878f7c099d2329 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ 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], diff --git a/NEWS b/NEWS index 0cdbb301f9a340bd5ab6651d42aa48808b321608..99126387ea2bf5ed0337daea38f29af4e159aa29 100644 --- a/NEWS +++ b/NEWS @@ -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 diff --git a/R/GOterms_heatmap.R b/R/GOterms_heatmap.R index f33729e6486470cfa74fc90c9d9c254fac52f42a..f21851d6d3fe753527fdb1573ec52a5b46df4fb5 100644 --- a/R/GOterms_heatmap.R +++ b/R/GOterms_heatmap.R @@ -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) diff --git a/R/runfgsea.R b/R/runfgsea.R index 349ff4d60d2ab6af15353d78d8923991ed8eda8e..9a4a0547947b734193d6d821fbe7efce45956760 100644 --- a/R/runfgsea.R +++ b/R/runfgsea.R @@ -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 diff --git a/README.md b/README.md index 92311f652e2b72df114140370ac89eeb56a087f7..a898703fbe549a9ea1fed1cec3991495c95a110f 100644 --- a/README.md +++ b/README.md @@ -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 diff --git a/man/runfgsea-methods.Rd b/man/runfgsea-methods.Rd index 6d3abb43799b4531e7bf17d983dd52c34e5b6555..f3d4f9b60d8d602db67c676438b8f66e5af0a065 100644 --- a/man/runfgsea-methods.Rd +++ b/man/runfgsea-methods.Rd @@ -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. diff --git a/vignettes/mouse_bioconductor.Rmd b/vignettes/mouse_bioconductor.Rmd index e4ef916f8afda7462cc5ddb1f8df4f19e5c055e4..7ba0b69a057b07235a9d038111088139304a6ad0 100644 --- a/vignettes/mouse_bioconductor.Rmd +++ b/vignettes/mouse_bioconductor.Rmd @@ -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(