Closed apelin20 closed 2 years ago
can you please share the input as an RDS file so that I can replicate the issue?
hello again, this was an issue with KEGGREST and they have recently resolved it. Please update via:
devtools::install_github("Bioconductor/KEGGREST")
Yes, the solution worked! I am happy they fixed KEGGREST. Here is how it looks now:
It's still a bit confusing because some gene are light green, any idea if there is a way to make all genes have white background unless FC information is given?
Unfortunately, KEGG restricts the number of genes to color. So for larger pathways it's currently not possible to color unchanged genes white. I'll try to find a work-around for this and keep you updated
Hey Ege, Is there any way to download KEGG directional interactions from somewhere? the .sif file? Or is that not available on purpose? Thanks, Adrian
On Tue, Jul 12, 2022 at 9:47 AM Ege Ulgen @.***> wrote:
Unfortunately, KEGG restricts the number of genes to color. So for larger pathways it's currently not possible to color unchanged genes white. I'll try to find a work-around for this and keep you updated
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Hey Adrian,Because pathfindR does not require directionality, that is not available in the package. I think the package KEGGREST (https://bioconductor.org/packages/release/bioc/html/KEGGREST.html) can be utilized for that purpose. Best,-EOn 13 Jun 2023, at 19:35, apelin20 @.***> wrote: Hey Ege,
Is there any way to download KEGG directional interactions from somewhere?
the .sif file? Or is that not available on purpose?
Thanks,
Adrian
On Tue, Jul 12, 2022 at 9:47 AM Ege Ulgen @.***> wrote:
Unfortunately, KEGG restricts the number of genes to color. So for larger
pathways it's currently not possible to color unchanged genes white. I'll
try to find a work-around for this and keep you updated
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https://github.com/egeulgen/pathfindR/issues/125#issuecomment-1182004840,
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Me again. I migrated to R4.2 and updated everything but am still having some issues.
I was to overlay my fold change data on KEGG maps (blue for downregulation and red for up).
For some reason, what is happening is all proteins in the KEGG map are colored light green instead of according to expression changes:
Focusing on a specific gene, TARF6, which should be red
Not sure what the last warning is about. I tried both normalize_vals as true and false, no difference.