upsetplot in clusterprofiler

Question

[Omics data mining]

Hi

I have 6 groups and did the enrichKEGG and enrichGO in clusterprofiler and got comparative output in dotplot format. I want get the output in upsetplot format. How can I see the comparative output in upsetplot format?

Thanks in advance

Archana

[Ram]

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.

[Omics data mining]

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.

[cpad0112]

@OP: You may want to post some example data (and expected image)

Answer 1

[Guangchuang Yu]

upsetplot is indeed supported, see http://bioconductor.org/packages/devel/bioc/vignettes/enrichplot/inst/doc/enrichplot.html#upset-plot.

[Omics data mining]

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

[Ram]

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.

[Ram]

Did you library() the package required for upsetplot()? I guess the package is DOSE, right?