Hello, I updated enrichplot, clusterprofiler, dose, geosemsim and installed ggtangle, however, all the emapplots are empty.
library(clusterProfiler)
library(enrichplot)
library(tidyverse)
library(org.Hs.eg.db) #org.Rn.eg.db #org.Hs.eg.db
library(RDAVIDWebService)
library(ggplot2)
library(pathview)
library(rrvgo)
library(GOSemSim)
library(ggtangle)
input_data <- read.csv("input.csv")
colnames(input_data)[1] <- "BACKGROUND"
background <- input_data$BACKGROUND
input_data$BACKGROUND <- NULL
cc_object <- compareCluster(geneCluster = input_data,
fun = "enrichGO",
OrgDb = organism,
keyType = "ENSEMBL",
minGSSize = 4,
maxGSSize = 400,
ont = "BP",
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.01,
universe = background)
amended_cc_object <- pairwise_termsim(cc_object)
set.seed(123456)
p1 <- emapplot(amended_cc_object, layout = igraph::layout_with_fr, showCategory=30, node_label = "category", group = FALSE,
group_style = "ggforce",
label_group_style = "shawdowtext",
label_format = 30,
clusterFunction = stats::kmeans,)
print(p1)
this is the code I use. I have used at least three datasets and emapplot is empty in all cases. It used to work on these before.
Hello, I updated enrichplot, clusterprofiler, dose, geosemsim and installed ggtangle, however, all the emapplots are empty.
this is the code I use. I have used at least three datasets and emapplot is empty in all cases. It used to work on these before.