update vignettes

DESCRIPTION

 Package: ViSEAGO
-Version: 1.3.9
+Version: 1.3.10
 Title: ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity
 Author: Aurelien Brionne [aut, cre],
         Amelie Juanchich [aut],

NEWS

@@ -74,4 +74,8 @@ CHANGES IN VERSION 1.3
  o merge_enrich_terms upgrade pvalue cutoff
  o merge_enrich_terms globale upgrade
  o GOterms_heatmap remove row side colors text
+ o vignettes update
+ o annotate() update for uniprot
+
+
 

R/GOclusters_heatmap.R

@@ -275,7 +275,7 @@ setMethod(
                 ticktext=row.text,
                 tickfont=list(size=10)
             ),
-            margin = list(l =300,r=0, b =150,t=50)
+            margin = list(l =300,r=0, b =150,t=100)
         )
 
         # hm to list

R/GOcount.R

@@ -142,7 +142,7 @@ setMethod(
             yaxis =list(
                 title =""
             ),
-             margin =list(b =100,l=150),
+             margin =list(t=100,b =100,l=150),
             title="number of significant (or not) GO terms by conditions",
             barmode = 'stack'
         )

R/GOterms_heatmap.R

@@ -908,7 +908,7 @@ setMethod(
             font=list(size=14),
 
             # set margin
-            margin=list(l=300,r=0,b=150,t=50)
+            margin=list(l=300,r=0,b=150,t=100)
         )
 
         # modify layout

R/MDSplot.R

@@ -182,6 +182,7 @@ setMethod(
                     levels=unique(res.mds$GO.cluster)
                 )
             }
+
         }else{
 
             # import SS_dist from object
@@ -219,7 +220,12 @@ setMethod(
             res.mds=rbindlist(res.mds)
 
             # custom text
-            res.mds[,`:=`("text"=res.mds$GO.cluster,GO.cluster=gsub("_.+$","",res.mds$GO.cluster))]
+            res.mds[,
+                `:=`(
+                    "text"=res.mds$GO.cluster,
+                    GO.cluster=gsub("_.+$","",res.mds$GO.cluster)
+                )
+            ]
 
             # add levels to measures
             res.mds$measure<-factor(
@@ -227,7 +233,7 @@ setMethod(
                 levels=unique(res.mds$measure)
             )
 
-            # add levels to GO.cluster
+            # add levels to GO.cluster 
             res.mds$GO.cluster<-factor(
                 res.mds$GO.cluster,
                 levels=unique(res.mds$GO.cluster)
@@ -292,6 +298,9 @@ setMethod(
                 xaxis=list(title="Dimension 1"),
                 yaxis=list(title="Dimension 2"),
 
+                # add margin
+                margin=list(t=100),
+
                 # add scrolling menu for availables measures
                 updatemenus = list(
 
@@ -347,6 +356,11 @@ setMethod(
                 sort=FALSE
             )
 
+            # ordering clusters
+            res.mds[,
+                GO.cluster:=factor(GO.cluster,levels=sort(unique(as.numeric(GO.cluster))))
+            ]
+
             # for terms
             if(type=="GOterms"){
 
@@ -378,7 +392,10 @@ setMethod(
 
                     # add axis legends
                     xaxis=list(title="Dimension 1"),
-                    yaxis=list(title="Dimension 2")
+                    yaxis=list(title="Dimension 2"),
+
+                    # add margin
+                    margin=list(t=100)
                 )
             }else{
 
@@ -425,6 +442,9 @@ setMethod(
           xaxis=list(title="Dimension 1"),
           yaxis=list(title="Dimension 2"),
 
+          # add margin
+          margin=list(t=100),
+
           # add scrolling menu for availables measures
           updatemenus = list(
 

R/Upset.R

@@ -67,18 +67,18 @@ setMethod(
                 Data,
                 sets=rev(names(Data)[-1]),
                 keep.order = TRUE,
-                text.scale=3
+                text.scale=2
             )
         )
 
         # print image to file
         png(sub("\\..+$",".png",file))
-            print(    
+            print(
                 upset(
                     Data,
                     sets=rev(names(Data)[-1]),
                     keep.order = TRUE,
-                    text.scale=3
+                    text.scale=2
                 )
             )
         dev.off()

R/annotate.R

@@ -389,7 +389,8 @@ setMethod(
                     sep=""
                 ),
                 destfile =temp,
-                quiet=TRUE
+                quiet=TRUE,
+                method="internal"
             )
 
             # unzip

README.md

@@ -27,7 +27,7 @@ remotes::install_gitlab(
     devtools::build("ViSEAGO")
 
     # install package (from R console)
-    install.packages("ViSEAGO_1.3.9.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_1.3.10.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation

vignettes/SS_choice.Rmd

@@ -2,11 +2,11 @@
 title: "Evaluate impact of Semantic Similiarity choice"
 author:
 - name: Aurelien Brionne
-  affiliation: Institut National de la Recherche Agronomique (INRA)
+  affiliation: "Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE)"
 - name: Amelie Juanchich
-  affiliation: Institut National de la Recherche Agronomique (INRA)
+  affiliation: "Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE)"
 - name: Christelle Hennequet-Antier
-  affiliation: Institut National de la Recherche Agronomique (INRA)
+  affiliation: "Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE)"
 date: "`r format(Sys.time(), '%d %B, %Y')`"
 output:
   BiocStyle::html_document: