issues with cnetplot from compareClusterResult

[guidohooiveld]

@GuangchuangYu

I am facing some issues when customizing the cnetplot that is generated from the results from a compareCluster analysis. Specifically, the size of the nodes cannot be increased. See plots below, specifically p4.

For comparison I have also included the output from cnetplot obtained after analyzing a single dataset (p1 - p2); these are all properly generated!

I believe this issue also relates to a similar issue reported for emapplot reported here: #308

Thanks in advance for having a look at this!

> library(clusterProfiler)
> library(enrichplot)
> library(org.Hs.eg.db)
> library(ggtangle)
> 
> ## example list of genes
> data(geneList, package="DOSE")
> genes <- names(geneList)[abs(geneList) > 2]
> 
> res <- enrichKEGG(gene = genes,
+                   organism = "hsa",
+                   keyType = "kegg",
+                   pvalueCutoff = 0.05,
+                   pAdjustMethod = "BH",
+                   minGSSize = 10,
+                   maxGSSize = 500)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> ## to increase readability, convert entrezid into symbols
> ## also calculate pairwise similarities (is in essence only applicable
> ## to GO terms, but just to be sure
> 
> res <- setReadable(res, OrgDb = org.Hs.eg.db, keyType="ENTREZID")
> res <- pairwise_termsim(res)
> 
> ## default plot
> p1 <- cnetplot(res,
+                layout = igraph::layout_nicely, ## default layout
+                showCategory = 3,
+                size_category = 1) ## default value
> print(p1)
> 

> ## increase size of 'category' to 4
> ## WORKS!
> p2 <- cnetplot(res,
+                layout = igraph::layout_nicely,
+                showCategory = 3,
+                size_category = 4)
> print(p2)
> 

> ###
> ## repeat, but now use output of compareCluster
> ###
> 
> ## load example input compareCluster 
> data(gcSample, package="clusterProfiler")
> 
> ck <- compareCluster(geneCluster = gcSample,
+                     fun = enrichKEGG,
+                     organism     = 'hsa',
+                     pvalueCutoff = 0.05)
> 
> ck <- setReadable(ck, OrgDb = org.Hs.eg.db, keyType="ENTREZID")
> ck <- pairwise_termsim(ck)
> 
> 
> ## default plot
> p3 <- cnetplot(ck,
+                layout = igraph::layout_nicely, ## default layout
+                showCategory = 1,
+                size_category = 1) ## default value
> print(p3)
Warning messages:
1: Removed 1204 rows containing non-finite outside the scale range (`stat_pie()`). 
2: ggrepel: 39 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
>

> ## increase size of 'category' to 4
> ## DOESN'T WORK! Node are not increased
> p4 <- cnetplot(ck,
+                layout = igraph::layout_nicely,
+                showCategory = 1,
+                size_category = 4)
> print(p4)
Warning messages:
1: Removed 1204 rows containing non-finite outside the scale range (`stat_pie()`). 
2: ggrepel: 37 unlabeled data points (too many overlaps). Consider increasing max.overlaps 
>