change edge color in cnetplot

[gqhhh]

Dear Yu group, I use cnetplot function and set the parameter 'colorEdge' as TRUE. But I would like to set my own colors of edge instead of the default color, how can I do that?

[guidohooiveld]

I realize that you have posted this a while ago,... Yet, for the archive:

With the current version of enrichplot you will need to use the argument color_edge, and provide the name (or hex code) of the color (default is: color_edge = "grey"). See ?cnetplot.

> library(clusterProfiler)
>  
> ## load example data
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
> 
> ## default analysis
> y1 <- enrichGO(de, 'org.Hs.eg.db',
+               ont = "CC",
+               pvalueCutoff = 0.05,
+               pAdjustMethod = "BH",
+               qvalueCutoff = 0.2)
> p1 <- cnetplot(y1, color_edge = "red", showCategory = 5)
> print(p1)
>

[paveliovidiu]

In a previus version I used to be able to color the edges by pathway and also have them show up in the legend. Has this been removed?

[guidohooiveld]

No, but you will need to set the argument color_edge to category (instead of the name of a color).

p2 <- cnetplot(y1, color_edge = "category", showCategory = 5)
print(p2)

[paveliovidiu]

Thanks! This is exactly what I needed.

[Charmy0619]

I am using v1.26.2, but color_edge = "category" doesn't work.

cnetplot(GOfile, node_label="all",showCategory=CatGO,categorySize="NES", categorySize="pvalue",foldChange = gene_list,circular = FALSE,color_edge = "category") +

• scale_colour_gradient2(name = "fold change", low = "blue", mid = "yellow", high = "red") Scale for colour is already present. Adding another scale for colour, which will replace the existing scale. Error: ! Problem while converting geom to grob. ℹ Error occurred in the 1st layer. Caused by error: ! Unknown colour name: category Run rlang::last_trace() to see where the error occurred.

This is a Gene Set Enrichment Analysis file, and I want to color the genes and edges. I can put the same color for all categories, but I want to use different colors for different categories. I am not sure how to do it in the new version.

[guidohooiveld]

Could you upload an example network (from a previous analysis [that apparently worked]) to show what you are after?

[guidohooiveld]

Got some time to prepare some examples. See also these threads: https://github.com/YuLab-SMU/enrichplot/issues/302#issuecomment-2517971618 and https://github.com/YuLab-SMU/enrichplot/issues/293#issuecomment-2462502566

> ## load libraries
> library(clusterProfiler)
> library(enrichplot)
> library(org.Hs.eg.db)
> 
> ## load example data
> data(geneList, package="DOSE")
> 
> ## reproducible example
> res <- gseGO(geneList      = geneList,
+              OrgDb         = org.Hs.eg.db,
+              keyType       = "ENTREZID",
+              ont           = "CC",
+              minGSSize     = 15,
+              maxGSSize     = 100,
+              eps           = 0,
+              pvalueCutoff  = 0.05,
+              pAdjustMethod = "BH")
using 'fgsea' for GSEA analysis, please cite Korotkevich et al (2019).

preparing geneSet collections...
GSEA analysis...
leading edge analysis...
done...
> 
> res <- pairwise_termsim(res)
> res <- setReadable(res, OrgDb = org.Hs.eg.db, keyType="ENTREZID")
> 
> 
> 
> ## select 5 *specific* sets to be plotted
> sets2plot <- as.data.frame(res)[c(1,3,4,7,8),]$Description
> sets2plot
[1] "spindle midzone"             "spindle microtubule"        
[3] "outer kinetochore"           "kinesin complex"            
[5] "complex of collagen trimers"
> 
> ## create cnetplot without node labels.
> ## these labels will be manually added
> ## using the function 'geom_cnet_label'
> 
> ## note: only the 5 sets in sets2plot are displayed
> p1 <- cnetplot(res, showCategory=sets2plot, node_label = "none", color_edge = "category", foldChange = geneList)
> print(p1)
> 

> ## add labels genes
> p2 <- p1 +
+    ggtangle::geom_cnet_label(node_label = "item", size = 2, fontface = "italic", color = "pink") 
> print(p2)
>

> ## add labels categories
> p3 <- p2 +
+    ggtangle::geom_cnet_label(node_label = "category", size = 6, fontface = "bold", color = "green")
> print(p3)
>

> ## alternatively, plot the top 10 sets,
> ## but only label those sets present in sets2plot
> p4 <- cnetplot(res, showCategory=10, node_label = "none", color_edge = "category", foldChange = geneList)
> print(p4)
> 

> p5 <- p4 +
+  ggtangle::geom_cnet_label(node_label = "item", size = 2, fontface = "italic", color = "gray")
> print(p5)
>

> p6 <- p5 +
+    ggtangle::geom_cnet_label(node_label = sets2plot, size = 3, fontface = "bold", color = "blue")
> print(p6)
>

> packageVersion("clusterProfiler")
[1] ‘4.14.6’
> packageVersion("enrichplot")
[1] ‘1.26.6’
> R.Version()$version.string
[1] "R version 4.4.2 (2024-10-31 ucrt)"
> BiocManager::version()
[1] ‘3.20’
> 

[billy-s-lab]

How do we control the edge aesthetic when coloured by category? I would like to change the edge colours from the ggplot default and also rename 'category' in the legend. I tried scale_colour_manual and ggraph::scale_edge_colour_manual to no effect. Thank you