How to extract network (in cnetplot + emapplot) for export?

[guidohooiveld]

Hi, For further fine-tuning of the layout (because of overlapping nodes/labels) I would like to export the underlying networks generated by the cnetplot and emapplot functions for further processing in (e.g.) Cytoscape.

1. I know that I can send igraph objects directly to Cytoscape using the RCy3 package. [Alternatively, the network could be exported as *.gml or *.graphml file].

2. From studying the relevant source codes I also know that under the hood first igraph objects are generated that are then 'further processed' within the functions (e.g. source code from cnetplot). Generation of the networks as igraph object: https://github.com/YuLab-SMU/enrichplot/blob/e2c76422a58b01637065e4b6f98e017ae690041a/R/cnetplot.R#L233 Example of further processing: https://github.com/YuLab-SMU/enrichplot/blob/e2c76422a58b01637065e4b6f98e017ae690041a/R/cnetplot.R#L240

So my question is if it currently is somehow possible to extract the "final" igraph object g from the output from the cnetplot and emapplot functions?

If so, how to do this?

If not, allow me then to submit a feature request; the (optional) addition of the igraph object g to the output from the cnetplot and emapplot functions (such as p below).

Thanks! G

> library(clusterProfiler)
> library(enrichplot)
> library(DOSE)
> 
> data(geneList)
> de <- names(geneList)[abs(geneList) > 2]
> 
> edo <- enrichDGN(de)
> 
> edox <- setReadable(edo, 'org.Hs.eg.db', 'ENTREZID')
> 
> p <- cnetplot(edox, color.params = list(foldChange = geneList) )
Scale for size is already present.
Adding another scale for size, which will replace the existing scale.
> 
> attributes(p)
$names
 [1] "data"        "layers"      "scales"      "mapping"     "theme"      
 [6] "coordinates" "facet"       "plot_env"    "labels"      "guides"     

$class
[1] "ggraph" "gg"     "ggplot"

> 

labels do overlap....