cnetplot with argument 'color_edge' doesn't work anymore with ggtangle 0.1.0 #341
Description
Hi,
I noticed that after updating ggtangle to v0.1.0 the argument color_edge within the fun cnetplot doesn't work anymore...
I am using the Bioconductor / CRAN release version of all libraries (thus not the development/GitHub ones).
Could you please have a look at this?
Thanks!
Reproducible code:
> library(clusterProfiler)
> library(enrichplot)
> library(DOSE)
> library(ggtangle)
>
> # Built-in dataset
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
>
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
> yy <- pairwise_termsim(yy)
> yy <- setReadable(yy, 'org.Hs.eg.db', 'ENTREZID')
>
> p1 <- cnetplot(yy, layout=igraph::layout_in_circle, showCategory = 4,
+ size_category = 0.5, color_edge = "category",
+ node_label="item", foldChange = geneList)
> p1
> print(p1)
>
> sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Amsterdam
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggtangle_0.0.9 DOSE_4.4.0 enrichplot_1.30.4
[4] clusterProfiler_4.18.4
With ggtangle v0.0.9:
After only updating ggtangle to v0.1.0 (all other packages remained the same!):
> library(clusterProfiler)
> library(enrichplot)
> library(ggtangle)
>
> # Built-in dataset
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:100]
>
> yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
> yy <- pairwise_termsim(yy)
> yy <- setReadable(yy, 'org.Hs.eg.db', 'ENTREZID')
>
> p1 <- cnetplot(yy, layout=igraph::layout_in_circle, showCategory = 4,
+ size_category = 0.5, color_edge = "category",
+ node_label="item", foldChange = geneList)
> p1
> print(p1)
> sessionInfo()
R version 4.5.1 (2025-06-13 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 22631)
Matrix products: default
LAPACK version 3.12.1
locale:
[1] LC_COLLATE=English_United States.utf8
[2] LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Europe/Amsterdam
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggtangle_0.1.0 DOSE_4.4.0 enrichplot_1.30.4
[4] clusterProfiler_4.18.4
