Entering edit mode
18 months ago
Omics data mining
▴
260
Hello everyone
I am trying to save graph (network) from cnetplot after enrichment analysis in clusterProfiler package. I want to develop network in cytoscape from saved network file.
> cnt_enrichment <- enrichplot::cnetplot(formula_res, circular = TRUE, colorEdge = TRUE,cex_label_gene = 0.5, cex_label_category =2,fixed=FALSE)
> attributes(cnt_enrichment)
$names
[1] "data" "layers" "scales" "mapping" "theme"
[6] "coordinates" "facet" "plot_env" "labels"
$class
[1] "ggraph" "gg" "ggplot"
Next, tried to export edge information from object.
> library(igraph)
Edata <- as.data.frame(get.edgelist(cnt_enrichment))
Edata$edgewidth <- E(g)$width
Vdata <- data.frame(pathway=V(g)$name, color=V(g)$color)
map_data <- list(edge_data=Edata, vertex_data=Vdata)
Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'as.data.frame': Not a graph object
I would appreciate all suggestion.
Thanks !!