diff --git a/DESCRIPTION b/DESCRIPTION
index fa54b4124180460485a5c3f23f54fce64cf020f6..37a3dad4b670432b851ea6552077bac207c33d82 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,5 +1,5 @@
 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],
diff --git a/NEWS b/NEWS
index db172128e1c60f34c1eb0a369e5c7f9739f58016..6d8fba23f1b3e4e21907437b7cb61d18b62fc9b6 100644
--- a/NEWS
+++ b/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
+
+
 
diff --git a/R/GOclusters_heatmap.R b/R/GOclusters_heatmap.R
index 67983dfab8717a22aab8af6812533e4272a5bf77..c14c59e0f5bfe123200eba64503a3f01220e6959 100644
--- a/R/GOclusters_heatmap.R
+++ b/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
diff --git a/R/GOcount.R b/R/GOcount.R
index 40ce30d3a76d3555a125b9fde98ba5ff3311f616..006e9552ed3d1ef377f71618b300ee21720d6bc0 100644
--- a/R/GOcount.R
+++ b/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'
         )
diff --git a/R/GOterms_heatmap.R b/R/GOterms_heatmap.R
index c93911bf9f5e64fbb6a7039eb107dbdaf6378d17..5153a1bd6e3d208a4501613d5e7b13271ff39ac1 100644
--- a/R/GOterms_heatmap.R
+++ b/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
diff --git a/R/MDSplot.R b/R/MDSplot.R
index 9c935dfb3ada92b488ddcd3148d714b971aab733..cd063ee4a2a62382faedf4194f942c498fe12b48 100644
--- a/R/MDSplot.R
+++ b/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(
 
diff --git a/R/Upset.R b/R/Upset.R
index 6c445d0862609623e6889b08a96ce665e370c067..7369badb769f4c1dfa236c243f9345b1206b06a1 100644
--- a/R/Upset.R
+++ b/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()
diff --git a/R/annotate.R b/R/annotate.R
index 8eb691f34244a5e50311e3553db81215ebcb20ed..6d825bdc6b999509077f90677d5bb6c6a42c1a47 100644
--- a/R/annotate.R
+++ b/R/annotate.R
@@ -389,7 +389,8 @@ setMethod(
                     sep=""
                 ),
                 destfile =temp,
-                quiet=TRUE
+                quiet=TRUE,
+                method="internal"
             )
 
             # unzip
diff --git a/README.md b/README.md
index 82dd035207aa5743603ff5042e5dd6089b267211..e53b2acf7c05f4dcb1d9d521e6f392326820dc1f 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_1.3.9.tar.gz", repos = NULL, type = "source")
+    install.packages("ViSEAGO_1.3.10.tar.gz", repos = NULL, type = "source")
 ```
 
 ## Citation
diff --git a/data/myGOs.RData b/data/myGOs.RData
index b9f676ceaf1eb630efdae7971156c03f9df5e554..565592f9e1252ee0addf6969a34f5d20afacfadc 100644
Binary files a/data/myGOs.RData and b/data/myGOs.RData differ
diff --git a/inst/extdata/data/output/bioconductor_BMA.png b/inst/extdata/data/output/bioconductor_BMA.png
index 2186778ca519f68bf0986b80dcb4741794b6a379..8156076cdf26ef1462ea7824279f91c1f8b35475 100644
Binary files a/inst/extdata/data/output/bioconductor_BMA.png and b/inst/extdata/data/output/bioconductor_BMA.png differ
diff --git a/inst/extdata/data/output/bioconductor_GOtermsheatmap.png b/inst/extdata/data/output/bioconductor_GOtermsheatmap.png
index 4710ebdae50c69ee0461b89ec74300c656f8a089..5b0df93f4378aa98d4f94ea5298e0a59c2a81464 100644
Binary files a/inst/extdata/data/output/bioconductor_GOtermsheatmap.png and b/inst/extdata/data/output/bioconductor_GOtermsheatmap.png differ
diff --git a/inst/extdata/data/output/bioconductor_mds1.png b/inst/extdata/data/output/bioconductor_mds1.png
index 8e2e4db199847841a3f136d6de07ae968c4259a0..22ef42ef0b0a237004d740a605079664cba620ec 100644
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diff --git a/inst/extdata/data/output/bioconductor_mds2.png b/inst/extdata/data/output/bioconductor_mds2.png
index 97799a2b679bbd6950bf6d00417335ec2df05fe6..b0afcad4dc7792f1af51b6d39e9ae86b03eb1cc8 100644
Binary files a/inst/extdata/data/output/bioconductor_mds2.png and b/inst/extdata/data/output/bioconductor_mds2.png differ
diff --git a/inst/extdata/data/output/bioconductor_mds3.png b/inst/extdata/data/output/bioconductor_mds3.png
index 48711131156253b8270e4ce2e3f9b9546644f0ef..02c5ed5ec39515c0420c021409e20f8831170dd5 100644
Binary files a/inst/extdata/data/output/bioconductor_mds3.png and b/inst/extdata/data/output/bioconductor_mds3.png differ
diff --git a/inst/extdata/data/output/bioconductor_table1.png b/inst/extdata/data/output/bioconductor_table1.png
index 3c2992b3ef28ed8bdfc9670dc5630adfa301556d..d7da5483cfb5ab826368b5ef891818fac2804add 100644
Binary files a/inst/extdata/data/output/bioconductor_table1.png and b/inst/extdata/data/output/bioconductor_table1.png differ
diff --git a/inst/extdata/data/output/bioconductor_table2.png b/inst/extdata/data/output/bioconductor_table2.png
index a627d8581f7d280d4f59236543b6a2303b1ad56f..d05950d25aa41756bb1f1298766349665bb37f08 100644
Binary files a/inst/extdata/data/output/bioconductor_table2.png and b/inst/extdata/data/output/bioconductor_table2.png differ
diff --git a/inst/extdata/data/output/gocount.png b/inst/extdata/data/output/gocount.png
index 0d08ea55e98788885309d56c1e69696fd9c23463..9d04ed480569c5b48653ef782b4b5e33bec3fb6a 100644
Binary files a/inst/extdata/data/output/gocount.png and b/inst/extdata/data/output/gocount.png differ
diff --git a/inst/extdata/data/output/upset.png b/inst/extdata/data/output/upset.png
index 6f7c5cad5463f1fd5854c635bd23cddd6d497ead..6d607d669da22970e471fc16aea9a43e973d9cc8 100644
Binary files a/inst/extdata/data/output/upset.png and b/inst/extdata/data/output/upset.png differ
diff --git a/vignettes/SS_choice.Rmd b/vignettes/SS_choice.Rmd
index 7403c74d291313329f3aa2c404c24ee287ef5aa5..3c5f69e4614b76b436dac07fe91b42147ed8e8f7 100644
--- a/vignettes/SS_choice.Rmd
+++ b/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:
diff --git a/vignettes/ViSEAGO.Rmd b/vignettes/ViSEAGO.Rmd
index 241b27538ab872434e2fb7a07c3bdc7f229b3c9b..0f29d5bc703ed067dda12b269ebb88e17c809c0c 100644
--- a/vignettes/ViSEAGO.Rmd
+++ b/vignettes/ViSEAGO.Rmd
@@ -2,11 +2,11 @@
 title: "An overview of ViSEAGO: Visualisation, Semantic similarity, Enrichment Analysis of Gene Ontology."
 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:
@@ -45,15 +45,8 @@ ViSEAGO is like a workflow with input lists of genes and associated genomic reso
 Firtsly, install the `r BiocStyle::Biocpkg("ViSEAGO")` R package from [Bioconductor](https://www.bioconductor.org/), or [ForgeMIA](https://forgemia.inra.fr/umr-boa/viseago) gitlab.
 
 ```{r ViSEAGO_install}
-# load ViSEAGO package from Bioconductor
+# Install ViSEAGO package from Bioconductor
 BiocManager::install("ViSEAGO")
-
-# load ViSEAGO package from gitLab
-remotes::install_gitlab(
-    "umr-boa/viseago",
-    host = "forgemia.inra.fr",
-    build_opts = c("--no-resave-data","--no-manual")
-)
 ```
 
 <u>NB:</u> This vignette is not runnable and provide a pseudo-code to illustrate ViSEAGO package capabilities.
diff --git a/vignettes/mouse_bionconductor.Rmd b/vignettes/mouse_bionconductor.Rmd
index 9201dadc9c9f1ff7f3bc8e1b88414160ba4ce99b..d9648f76ec3e7c126ddf87af618860b046b07c64 100644
--- a/vignettes/mouse_bionconductor.Rmd
+++ b/vignettes/mouse_bionconductor.Rmd
@@ -2,11 +2,11 @@
 title: "Functional analysis of mouse mammary gland RNA-Seq"
 author:
 - name: Aurelien Brionne
-  affiliation: BOA, Institut National de la Recherche Agronomique (INRA), Universitée de Tours, 37380 Nouzilly, France
+  affiliation: "Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE)"
 - name: Amelie Juanchich
-  affiliation: BOA, Institut National de la Recherche Agronomique (INRA), Universitée de Tours, 37380 Nouzilly, France
+  affiliation: "Institut national de recherche pour l'agriculture, l'alimentation et l'environnement (INRAE)"
 - name: Christelle Hennequet-Antier
-  affiliation: BOA, Institut National de la Recherche Agronomique (INRA), Universitée de Tours, 37380 Nouzilly, France
+  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:
@@ -129,13 +129,13 @@ myGENE2GO
 cat(
 "- object class: gene2GO
 - database: Bioconductor
-- stamp/version: 2018-Oct11
+- stamp/version: 2019-Jul10
 - organism id: org.Mm.eg.db
 
 GO annotations:
-- Molecular Function (MF): 22744 annotated genes with 90922 terms (4133 unique terms)
-- Biological Process (BP): 23239 annotated genes with 160094 terms (12087 unique terms)
-- Cellular Component (CC): 23416 annotated genes with 105430 terms (1727 unique terms)"  
+- Molecular Function (MF): 22707 annotated genes with 91986 terms (4121 unique terms)
+- Biological Process (BP): 23210 annotated genes with 164825 terms (12224 unique terms)
+- Cellular Component (CC): 23436 annotated genes with 107852 terms (1723 unique terms)"
 )
 ```
 
@@ -235,17 +235,7 @@ BP_sResults
 </br>
 ```{r Enrichment_merge_display,echo=FALSE,eval=TRUE}
 cat(
-"- object class: gene2GO
-- database: Bioconductor
-- stamp/version: 2018-Apr4
-- organism id: org.Mm.eg.db
-
-GO annotations:
-- Molecular Function (MF): 23049 annotated genes with 92018 terms (4118 unique terms)
-- Biological Process (BP): 23843 annotated genes with 162583 terms (11881 unique terms)
-- Cellular Component (CC): 23583 annotated genes with 102801 terms (1662 unique terms)
-> BP_sResults
-- object class: enrich_GO_terms
+"- object class: enrich_GO_terms
 - ontology: BP
 - input:
         PregnantvsLactate: elim
@@ -254,69 +244,69 @@ GO annotations:
 - topGO summary:
  PregnantvsLactate
       BP_PregnantvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 7699
-        feasible_genes: 14402
-        feasible_genes_significant: 7185
+        feasible_genes: 14091
+        feasible_genes_significant: 7044
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_PregnantvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 198
-        feasible_genes: 14402
-        feasible_genes_significant: 7185
+        GO_scored: 8463
+        GO_significant: 199
+        feasible_genes: 14091
+        feasible_genes_significant: 7044
         genes_nodeSize: 5
-        Nontrivial_nodes: 8155 
+        Nontrivial_nodes: 8433 
  VirginvsLactate
       BP_VirginvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 9583
-        feasible_genes: 14402
-        feasible_genes_significant: 8898
+        feasible_genes: 14091
+        feasible_genes_significant: 8734
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_VirginvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 151
-        feasible_genes: 14402
-        feasible_genes_significant: 8898
+        GO_scored: 8463
+        GO_significant: 152
+        feasible_genes: 14091
+        feasible_genes_significant: 8734
         genes_nodeSize: 5
-        Nontrivial_nodes: 8180 
+        Nontrivial_nodes: 8457 
  VirginvsPregnant
       BP_VirginvsPregnant 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 7302
-        feasible_genes: 14402
-        feasible_genes_significant: 6875
+        feasible_genes: 14091
+        feasible_genes_significant: 6733
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_VirginvsPregnant 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 232
-        feasible_genes: 14402
-        feasible_genes_significant: 6875
+        GO_scored: 8463
+        GO_significant: 243
+        feasible_genes: 14091
+        feasible_genes_significant: 6733
         genes_nodeSize: 5
-        Nontrivial_nodes: 8143 
+        Nontrivial_nodes: 8413 
  
-- enrich GOs data.table (p<0.01 in at least one list): 509 GO terms of 3 conditions.
-        PregnantvsLactate : 198 terms
-        VirginvsLactate : 151 terms
-        VirginvsPregnant : 232 terms"
+- enrich GOs (in at least one list): 521 GO terms of 3 conditions.
+        PregnantvsLactate : 199 terms
+        VirginvsLactate : 152 terms
+        VirginvsPregnant : 243 terms"
 )
 ```
 </br>
@@ -377,7 +367,7 @@ myGOs
 cat(
 "- object class: GO_SS
 - database: Bioconductor
-- stamp/version: 2018-Apr4
+- stamp/version: 2019-Jul10
 - organism id: org.Mm.eg.db
 - ontology: BP
 - input:
@@ -387,69 +377,69 @@ cat(
 - topGO summary:
  PregnantvsLactate
       BP_PregnantvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 7699
-        feasible_genes: 14402
-        feasible_genes_significant: 7185
+        feasible_genes: 14091
+        feasible_genes_significant: 7044
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_PregnantvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 198
-        feasible_genes: 14402
-        feasible_genes_significant: 7185
+        GO_scored: 8463
+        GO_significant: 199
+        feasible_genes: 14091
+        feasible_genes_significant: 7044
         genes_nodeSize: 5
-        Nontrivial_nodes: 8155 
+        Nontrivial_nodes: 8433 
  VirginvsLactate
       BP_VirginvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 9583
-        feasible_genes: 14402
-        feasible_genes_significant: 8898
+        feasible_genes: 14091
+        feasible_genes_significant: 8734
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_VirginvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 151
-        feasible_genes: 14402
-        feasible_genes_significant: 8898
+        GO_scored: 8463
+        GO_significant: 152
+        feasible_genes: 14091
+        feasible_genes_significant: 8734
         genes_nodeSize: 5
-        Nontrivial_nodes: 8180 
+        Nontrivial_nodes: 8457 
  VirginvsPregnant
       BP_VirginvsPregnant 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 7302
-        feasible_genes: 14402
-        feasible_genes_significant: 6875
+        feasible_genes: 14091
+        feasible_genes_significant: 6733
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_VirginvsPregnant 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 232
-        feasible_genes: 14402
-        feasible_genes_significant: 6875
+        GO_scored: 8463
+        GO_significant: 243
+        feasible_genes: 14091
+        feasible_genes_significant: 6733
         genes_nodeSize: 5
-        Nontrivial_nodes: 8143 
- 
-- enrich GOs data.table: 509 GO terms of 3 conditions.
-        PregnantvsLactate : 198 terms
-        VirginvsLactate : 151 terms
-        VirginvsPregnant : 232 terms
+        Nontrivial_nodes: 8413 
+
+- enrich GOs data.table: 521 GO terms of 3 conditions.
+        PregnantvsLactate : 199 terms
+        VirginvsLactate : 152 terms
+        VirginvsPregnant : 243 terms
 - terms distances:  Wang"
 )
 ```
@@ -514,7 +504,9 @@ The printed table contains for each enriched GO terms, additional columns includ
 
 ```{r SS_Wang-ward.D2_table}
 # display table
-ViSEAGO::show_table(Wang_clusters_wardD2)
+ViSEAGO::show_table(
+    Wang_clusters_wardD2
+)
 ```
 
 <img src=`r system.file("extdata/data/output","bioconductor_table2.png",package="ViSEAGO")` alt="bioconductor_table2" style="width:100%;height:100%;"/>
@@ -527,7 +519,10 @@ We also display a colored Multi Dimensional Scale (MDS) plot showing the overlay
 
 ```{r SS_Wang-ward.D2_mdsplot}
 # colored MDSplot
-ViSEAGO::MDSplot(Wang_clusters_wardD2)
+ViSEAGO::MDSplot(
+    Wang_clusters_wardD2,
+    "GOterms"
+)
 ```
 
 <img src=`r system.file("extdata/data/output","bioconductor_mds2.png",package="ViSEAGO")` alt="mds2" style="width:100%;height:100%;"/>
@@ -598,7 +593,7 @@ Wang_clusters_wardD2
 cat(
 "- object class: GO_clusters
 - database: Bioconductor
-- stamp/version: 2018-Apr4
+- stamp/version: 2019-Jul10
 - organism id: org.Mm.eg.db
 - ontology: BP
 - input:
@@ -608,69 +603,69 @@ cat(
 - topGO summary:
  PregnantvsLactate
       BP_PregnantvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 7699
-        feasible_genes: 14402
-        feasible_genes_significant: 7185
+        feasible_genes: 14091
+        feasible_genes_significant: 7044
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_PregnantvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 198
-        feasible_genes: 14402
-        feasible_genes_significant: 7185
+        GO_scored: 8463
+        GO_significant: 199
+        feasible_genes: 14091
+        feasible_genes_significant: 7044
         genes_nodeSize: 5
-        Nontrivial_nodes: 8155 
+        Nontrivial_nodes: 8433 
  VirginvsLactate
       BP_VirginvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 9583
-        feasible_genes: 14402
-        feasible_genes_significant: 8898
+        feasible_genes: 14091
+        feasible_genes_significant: 8734
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_VirginvsLactate 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 151
-        feasible_genes: 14402
-        feasible_genes_significant: 8898
+        GO_scored: 8463
+        GO_significant: 152
+        feasible_genes: 14091
+        feasible_genes_significant: 8734
         genes_nodeSize: 5
-        Nontrivial_nodes: 8180 
+        Nontrivial_nodes: 8457 
  VirginvsPregnant
       BP_VirginvsPregnant 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4
+        description: Bioconductor org.Mm.eg.db 2019-Jul10
         available_genes: 15804
         available_genes_significant: 7302
-        feasible_genes: 14402
-        feasible_genes_significant: 6875
+        feasible_genes: 14091
+        feasible_genes_significant: 6733
         genes_nodeSize: 5
-        nodes_number: 8189
-        edges_number: 18887
+        nodes_number: 8463
+        edges_number: 19543
       elim_BP_VirginvsPregnant 
-        description: Bioconductor org.Mm.eg.db 2018-Apr4 
+        description: Bioconductor org.Mm.eg.db 2019-Jul10 
         test_name: fisher p<0.01
         algorithm_name: elim
-        GO_scored: 8189
-        GO_significant: 232
-        feasible_genes: 14402
-        feasible_genes_significant: 6875
+        GO_scored: 8463
+        GO_significant: 243
+        feasible_genes: 14091
+        feasible_genes_significant: 6733
         genes_nodeSize: 5
-        Nontrivial_nodes: 8143 
+        Nontrivial_nodes: 8413 
  
-- enrich GOs data.table: 509 GO terms of 3 conditions.
-        PregnantvsLactate : 198 terms
-        VirginvsLactate : 151 terms
-        VirginvsPregnant : 232 terms
+- enrich GOs data.table: 521 GO terms of 3 conditions.
+        PregnantvsLactate : 199 terms
+        VirginvsLactate : 152 terms
+        VirginvsPregnant : 243 terms
 - clusters distances: BMA
 - Heatmap:
           * GOterms: TRUE
@@ -681,10 +676,10 @@ cat(
                               cut.dynamic.pamRespectsDendro: TRUE
                               cut.dynamic.deepSplit: 2
                               cut.dynamic.minClusterSize: 2
-                              number of clusters: 56
-                              clusters min size: 1
-                              clusters mean size: 30
-                              clusters max size: 56
+                              number of clusters: 62
+                              clusters min size: 2
+                              clusters mean size: 8
+                              clusters max size: 32
                    - sample.tree: FALSE
           * GOclusters: TRUE
                        - tree: