Package: clusterProfiler by Guangchuang Yu
Let start with the example code (just the same as from the vignette):
library(clusterProfiler) library(enrichplot) # basic analysis data(geneList, package="DOSE") kegg <- gseKEGG(geneList = geneList, organism = 'hsa') # plotting cnetplot(kegg, categorySize="pvalue", foldChange=geneList)
I want to change two things in this cnetplot
- Exclude pathways in the graph
- Providing gene names instead of the IDs
1. Using the example:
require(dplyr) head(kegg@result) %>% select(Description, setSize) Description setSize hsa04510 Focal adhesion 188 hsa00982 Drug metabolism - cytochrome P450 49 hsa03050 Proteasome 42 hsa03030 DNA replication 33 hsa05340 Primary immunodeficiency 34 hsa04151 PI3K-Akt signaling pathway 320
Let's say I do not want the genes for the Focal adhesion
in the cnet graph, how can this be accomplished.
2. using the example
Instead of the ids (such as 6891
) I want to show the gene names which I provide myself (or maybe this can be done automatically)
Dear Guangchuang Yu,
Regarding question 1:
The version I currently have is
enrichplot_1.1.1.001
, which is >=1.0.1 as recommended by you. However when I pass a vector of pathway names to thecnetplot
command ( like sox <- cnetplot(kegg, showCategory = kegg$Description[-2])
) it will give this error:Can't figure out what I'm doing wrong here.
Regarding question 2:
After re-reading this question I think I wasn't that clear with what I mean. I love that function, however what I meant is that I could pass this to
cnetplot
. Of course I could convert the ids to the gene names before calling thegseKEGG
function, but this will probably interfere with mapping. Therefore, I want to be able to pass the gene names tocnetplot
pls use enrichplot v >= 1.0.2 or v >= 1.1.2, which address the issue you reported.
you misunderstand how setReadable works.
1. Thankyou! that version seems to work fine
2. The setReadable will of course only work whenever a db is available for the species in question, this is not the case for me. Therefore I mentioned
gene names which I provide myself
in my question I looked at the code of and thought I could easily mimic the setReadable function like so:However this will still only show the ids (and loses coloring in the network), instead the names I provided in the
gene.name.vector
, is there any way to provide these manually?