Struggling to use the compare cluster function in Cluster Profiler

Question

[S'bonelo Glen]

Hi everyone

I want to generate a dot plot by comparing different enriched pathways and GO terms (BP) across a list of tissues collected from the mouse model. I tried using the compare cluster function in Cluster Profiler, but I kept on getting an error. Here is the data (https://docs.google.com/spreadsheets/d/1AqGDLLLb7FDqCZg8bPhpAV3wNYFGy2bc/edit?usp=drive_link&ouid=118139446396256084376&rtpof=true&sd=true)

See script below:

df <- as.list(DEPs_unique)
str(df)

ck <- compareCluster(geneCluster = df, fun = enrichKEGG)

ck <- setReadable(ck, OrgDb = org.Mm.eg.db, keyType = "SYMBOL")

head(ck)

When I run the code, I get this warning messages:

1: In utils::download.file(url, quiet = TRUE, method = method, ...) :
  the 'wininet' method is deprecated for http:// and https:// URLs
2: In utils::download.file(url, quiet = TRUE, method = method, ...) :
  the 'wininet' method is deprecated for http:// and https:// URLs
3: In compareCluster(geneCluster = df, fun = enrichKEGG) :
  No enrichment found in any of gene cluster, please check your input...