Entering edit mode
20 days ago
Dr Huma Naz
•
0
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
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