How can I display fold change values in my Gene-Concept Network in R?

[Adam52]

I am currently developing a Gene-Concept Network plot in R after running differential gene expression analysis on an extensive dataset using the following code which displays a simple plot:

cnetplot(gsea_msigdb_h)

However, I would like to display fold change values so my plot appears similar to the one on this site: Visualization of Functional Enrichment Result.

I tried implementing the following modified code in R based on the suggestion from this site but received the following error:

cnetplot(gsea_msigdb_h,foldChange=geneList) Error in fc_readable(x,
foldChange) : object 'geneList' not found

Any suggestions on how I can modify my code to display colour coded fold change values?

[Dalsbo83]

Look I am no expert in enrichment analysis (or R) and I have not worked with this package.

however, I would like to give a try

I hate to state the obvious, but it seems you do not have an object called geneList

The geneList seems to be a vector with entrez gene number identifiers and their respective fold change. There is an example dataset in the DOSE package from bioconductor called exactly that: "geneList"

Try to make a similar vector
Maybe you have a table or something containing gene number and fold changes
make a vector from the fold change column and name it using the ID number column.

Then use this vector as the foldChange argument

something like

listgenes <- sometable$foldchange
names(listgenes) <- sometable$ID_numbers

cnetplot(gsea_msigdb_h,foldChange=listgenes)

Note: this will not run! Change code according to your naming I do not know your environment setup

Just an idea. Maybe it works.