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Mr.RB
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@mrrb-15633
Last seen 5.6 years ago
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 thecnetplotcommand ( 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 thegseKEGGfunction, but this will probably interfere with mapping. Therefore, I want to be able to pass the gene names tocnetplotpls 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 myselfin 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?Dear Guangchuang Yu, Can cnetplot just show the common genes between pathways? There are so many unique genes that the results are hard to read.