show_heatmap upgrade

DESCRIPTION

 Package: ViSEAGO
-Version: 1.3.2
+Version: 1.3.3
 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
 Author: Aurelien Brionne [aut, cre],
         Amelie Juanchich [aut],

NEWS

@@ -69,4 +69,5 @@ CHANGES IN VERSION 1.3
 ------------------------
  o print graph with orca
  o Ensembl2GO() biomart update
+ o show_heatmap() upgrade
 

R/show_heatmap.R

@@ -8,9 +8,12 @@
 #' @param object a \code{\link{GO_clusters-class}} object from \code{\link{GOterms_heatmap}} or \code{\link{GOclusters_heatmap}}.
 #' @param type could be "GOterms" to display GOterms clustering heatmap, or "GOclusters" to display GOclusters heatmap.
 #' @param file static image output file name (default to NULL).
+#' @param plotly_update update plotly html dependencies (default to FALSE).
 #' @details
 #' This method displays an interactive heatmap (if \code{file}=NULL) from \code{\link{GO_clusters-class}} object for "GOterms" or "GOclusters" type.\cr
-#' A static png image could be printed by setting \code{file} argument.
+#' A static png image could be printed by setting \code{file} argument.\cr
+#' Interactive heatmap cannot be displayed between two R versions.
+#' Then interactive view (build with previous R version) can be updated to new R version using \code{plotly_update} argument setting to TRUE.
 #' @return display or print heatmap.
 #' @examples
 #' # load data example
@@ -98,7 +101,7 @@
 #' @exportMethod show_heatmap
 setGeneric(
     name="show_heatmap",
-    def=function(object,type,file=NULL) {
+    def=function(object,type,file=NULL,plotly_update=FALSE) {
         standardGeneric("show_heatmap")
     }
 )
@@ -111,7 +114,7 @@ setMethod(
         object="GO_clusters",
         type="character"
     ),
-    definition=function(object,type,file){
+    definition=function(object,type,file,plotly_update){
 
         # check type argument
         type=match.arg(type,c("GOterms","GOclusters"))
@@ -126,6 +129,18 @@ setMethod(
             GOclusters=slot(object,"heatmap")$GOclusters
         )
 
+        # redirect plotly html_dependency to local packages
+        if(plotly_update==TRUE){
+
+            for(i in seq_len(length(heatmap[["dependencies"]]))){
+                heatmap[["dependencies"]][[i]][["src"]][["file"]]<-gsub(
+                    "^.+[[:digit:]]\\.[[:digit:]]",
+                    .libPaths()[1],
+                    heatmap[["dependencies"]][[i]][["src"]][["file"]]
+                )
+            }
+        }
+
         # return interactive or static heatmap according file
         if(is.null(file)){
 

README.md

@@ -27,7 +27,7 @@ remotes::install_gitlab(
     devtools::build("ViSEAGO")
 
     # install package (from R console)
-    install.packages("ViSEAGO_1.3.2.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_1.3.3.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation

man/show_heatmap-methods.Rd

@@ -5,9 +5,9 @@
 \alias{show_heatmap,GO_clusters,character-method}
 \title{Display an interactive or static heatmap.}
 \usage{
-show_heatmap(object, type, file = NULL)
+show_heatmap(object, type, file = NULL, plotly_update = FALSE)
 
-\S4method{show_heatmap}{GO_clusters,character}(object, type, file = NULL)
+\S4method{show_heatmap}{GO_clusters,character}(object, type, file = NULL, plotly_update = FALSE)
 }
 \arguments{
 \item{object}{a \code{\link{GO_clusters-class}} object from \code{\link{GOterms_heatmap}} or \code{\link{GOclusters_heatmap}}.}
@@ -15,6 +15,8 @@ show_heatmap(object, type, file = NULL)
 \item{type}{could be "GOterms" to display GOterms clustering heatmap, or "GOclusters" to display GOclusters heatmap.}
 
 \item{file}{static image output file name (default to NULL).}
+
+\item{plotly_update}{update plotly html dependencies (default to FALSE).}
 }
 \value{
 display or print heatmap.
@@ -24,7 +26,9 @@ Display a heatmap in interactive or static mode.
 }
 \details{
 This method displays an interactive heatmap (if \code{file}=NULL) from \code{\link{GO_clusters-class}} object for "GOterms" or "GOclusters" type.\cr
-A static png image could be printed by setting \code{file} argument.
+A static png image could be printed by setting \code{file} argument.\cr
+Interactive heatmap cannot be displayed between two R versions.
+Then interactive view (build with previous R version) can be updated to new R version using \code{plotly_update} argument setting to TRUE.
 }
 \examples{
 # load data example