after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.

Question

[Dr Huma Naz]

Hi team,

I am using cneplot for visualizing specific GO terms from clusterprofiler object. After selecting specific terms, cneplot is black and white without any nodes. only showing gene and terms names and lines between them. nodes are not showing up.

These are package details and codes I used.

library(RColorBrewer) # colorRampPalette()
library(clusterProfiler)
library(VennDiagram)
library(ggplot2)
#BiocManager::install("org.Mm.eg.db")
library(org.Mm.eg.db)
library(Hmisc) # for capitalize
library(Seurat)
library(SeuratObject)
library(DOSE)
library(AnnotationDbi)
library(enrichplot)
library(pathview)

#obj is
List_DEG_EdU_Microglia_compGO_ALL

ego <- List_DEG_EdU_Microglia_compGO_ALL@compareClusterResult
#select specific terms to plot
x <- ego[ego$Description %in% c("neuroinflammatory response", "microglial cell activation", "negative regulation of immune system process"), ]

Selecetd_List_DEG_EdU_Microglia_compGO_ALL <- List_DEG_EdU_Microglia_compGO_ALL

Selecetd_List_DEG_EdU_Microglia_compGO_ALL@compareClusterResult <- x

cnetplot(Selecetd_List_DEG_EdU_Microglia_compGO_ALL, colorEdge = TRUE,categorySize="pvalue",cex_label_category= 2, cex_label_gene =2,layout = "kk", color_category = "#97c497", node_label = "all")

cneplot with specific terms:

As you can see there is no color for genes and terms and even nodes are not appearing. Please help

Thanks

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or use one of (a) the option highlighted in the image below/ (b) fenced code blocks for multi-line code. Fenced code blocks are useful in syntax highlighting. If your code has long lines with a single command, break those lines into multiple lines with proper escape sequences so they're easier to read and still run when copy-pasted. I've done it for you this time.