Hi Thx for your reply . Here is my code ,
c1 <- read.table("c1.txt",header=T)
c1g <- c1$c1
c1gg <- as.character(c1g)
c1eg = bitr(c1gg, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db")
c2 <- read.table("c2.txt",header=T)
c2g <- c2$c2
c2gg <- as.character(c2g)
c2eg = bitr(c2gg, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Hs.eg.db")
kegg <- list(x1=c1eg$ENTREZID,x2=c2eg$ENTREZID)
ck_kegg <- compareCluster(geneCluster = kegg, fun = "enrichKEGG" )
barplot(ck_kegg)
Here I can get the comapritive barplot. But for
upsetplot(ck_kegg)
Error in upsetplot(ck_kegg) : could not find function "upsetplot"
Is there anything I am missing ? Is Upsetplot compatible with comaprecluster results ?
Thank you
Archana
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Ram
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Omics data mining
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Omics data mining
I'm not sure about clusterprofiler, but most tools that give you a plot will also give you the data that drives the plot, which could be used to create a plot of your liking. Is this not the case with clusterprofiler?
Also, please proof-read your post before you submit - that should avoid typos. I've corrected them this time.
Hi Ram
Upsetplot is supported in clusterprofiler as indicated in visulisation https://bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html. For me its not working. I tring to fix it.
@OP: You may want to post some example data (and expected image)