Has this plot been removed in the latest version of the R package?

[JWDu0122]

Has this plot been removed in the latest version of the R package? I am now unable to generate this plot. My code is: cnetplot(bp,showCategory=10,circular=TRUE,colorEdge=TRUE)

[guidohooiveld]

You can still make these plots. See code below.

Also have a look at e.g. this post/thread, because it will show how to customize your plot regarding many aspects using the function geom_cnet_label().
YuLab-SMU/enrichplot#302

Note: I used the release version of clusterProfiler and enrichplot available at Bioconductor! (Thus not the development version of the packages that are on GitHub).

p2

> library(clusterProfiler)
> library(enrichplot)
> 
> data(geneList, package = "DOSE")
> de <- names(geneList)[1:150]
> 
> yy <- enrichKEGG(de, pvalueCutoff=0.05)
Reading KEGG annotation online: "https://rest.kegg.jp/link/hsa/pathway"...
Reading KEGG annotation online: "https://rest.kegg.jp/list/pathway/hsa"...
> yy <- setReadable(yy, 'org.Hs.eg.db', 'ENTREZID')

> 
> ## using 2 steps to customize the labels of the categories (gene sets).
> p1 <- cnetplot(yy, layout=igraph::layout_in_circle, showCategory = 5,
+                size_category = 0.5, color_edge = "category", 
+                node_label="item", foldChange = geneList)
> 
> p2 <- p1 + geom_cnet_label(node_label = "category",  size = 5,
+            color = "blue", fontface = "bold.italic")
> 
> print(p2)
> 
> 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] enrichplot_1.30.4      clusterProfiler_4.18.4

loaded via a namespace (and not attached):
  [1] DBI_1.2.3               gson_0.1.0              rlang_1.1.6            
  [4] magrittr_2.0.4          DOSE_4.4.0              compiler_4.5.1         
  [7] RSQLite_2.4.5           png_0.1-8               systemfonts_1.3.1      
 [10] vctrs_0.6.5             reshape2_1.4.5          stringr_1.6.0          
 [13] pkgconfig_2.0.3         crayon_1.5.3            fastmap_1.2.0          
 [16] XVector_0.50.0          labeling_0.4.3          purrr_1.2.0            
 [19] bit_4.6.0               cachem_1.1.0            aplot_0.2.9            
 [22] jsonlite_2.0.0          blob_1.2.4              tidydr_0.0.6           
 [25] BiocParallel_1.44.0     tweenr_2.0.3            parallel_4.5.1         
 [28] cluster_2.1.8.1         R6_2.6.1                stringi_1.8.7          
 [31] RColorBrewer_1.1-3      GOSemSim_2.36.0         Rcpp_1.1.0             
 [34] Seqinfo_1.0.0           ggtangle_0.0.9          R.utils_2.13.0         
 [37] IRanges_2.44.0          Matrix_1.7-4            splines_4.5.1          
 [40] igraph_2.2.1            tidyselect_1.2.1        qvalue_2.42.0          
 [43] dichromat_2.0-0.1       codetools_0.2-20        lattice_0.22-7         
 [46] tibble_3.3.0            plyr_1.8.9              Biobase_2.70.0         
 [49] treeio_1.34.0           withr_3.0.2             KEGGREST_1.50.0        
 [52] S7_0.2.1                gridGraphics_0.5-1      scatterpie_0.2.6       
 [55] polyclip_1.10-7         Biostrings_2.78.0       pillar_1.11.1          
 [58] ggtree_4.0.3            stats4_4.5.1            ggfun_0.2.0            
 [61] generics_0.1.4          S4Vectors_0.48.0        ggplot2_4.0.1          
 [64] scales_1.4.0            tidytree_0.4.6          glue_1.8.0             
 [67] gdtools_0.4.4           lazyeval_0.2.2          tools_4.5.1            
 [70] ggnewscale_0.5.2        data.table_1.18.0       fgsea_1.36.0           
 [73] ggiraph_0.9.2           fs_1.6.6                fastmatch_1.1-6        
 [76] cowplot_1.2.0           grid_4.5.1              tidyr_1.3.2            
 [79] ape_5.8-1               AnnotationDbi_1.72.0    nlme_3.1-168           
 [82] patchwork_1.3.2         ggforce_0.5.0           cli_3.6.5              
 [85] rappdirs_0.3.3          fontBitstreamVera_0.1.1 dplyr_1.1.4            
 [88] gtable_0.3.6            R.methodsS3_1.8.2       yulab.utils_0.2.3      
 [91] digest_0.6.39           fontquiver_0.2.1        BiocGenerics_0.56.0    
 [94] ggrepel_0.9.6           ggplotify_0.1.3         org.Hs.eg.db_3.22.0    
 [97] htmlwidgets_1.6.4       farver_2.1.2            memoise_2.0.1          
[100] htmltools_0.5.9         R.oo_1.27.1             lifecycle_1.0.4        
[103] httr_1.4.7              GO.db_3.22.0            fontLiberation_0.1.0   
[106] bit64_4.6.0-1           MASS_7.3-65            
> 

[guidohooiveld]

Addition: to increase readability you could do for example insert this line after generation of yy:
yy@result$Description <- stringr::str_wrap( yy@result$Description, width=25)
(it will insert a new line after every 25 characters. Note that a function of the library stringr is used for this).

Thus:

> yy@result$Description <- stringr::str_wrap( yy@result$Description, width=25)
> ## using 2 steps to customize the labels of the categories (gene sets).
> p1 <- cnetplot(yy, layout=igraph::layout_in_circle, showCategory = 4,
+                size_category = 0.5, color_edge = "category", 
+                node_label="item", foldChange = geneList)
> 
> p2 <- p1 + geom_cnet_label(node_label = "category",  size = 5,
+            color = "blue", fontface = "bold.italic")
> 
> print(p2)
> 

Will give...