noriakis comments

Results 22 comments of


                                            noriakis

"I would like to know why I encounter these missing values when plotting certain pathways?"

Hi, thanks for the report! Could you provide me with the codes you used to produce the figure?

"I would like to know why I encounter these missing values when plotting certain pathways?"

Hi, thanks for the reply, but could you paste the code here as I cannot tell which example you tried?

"I would like to know why I encounter these missing values when plotting certain pathways?"

Hi, closing the issue but feel free to reopen it!

directory not work

Thanks for reaching out and I am sorry for the very late response. Could you provide the code? `highlight_module` itself does not download the module file.

directory not work

Hi, closing the issue but feel free to reopen it if the problem persists.

Can I highlight pathway instead of modules in pathway?

Hi @ucabuk, Thank you for raising this point. This is an important problem. Node highlighting would be easy as we need to simply take all the elements in one pathway...

Does CBNplot Discretize Input VSD Data During Network Construction?

Hi, Thanks for reaching out. CBNplot does not discretize the data by default. If the `disc` option is set to TRUE, the function discretizes the continuous input using `arules::discretize`. I...

Error message with the example "The plot with the reference"

Dear @zyb1984, I sincerely appreciate your detailed feedback and code. I apologize for the error and my delayed response. Currently, the package is undergoing the reviewing process of Bioconductor and...

Error message with the example "The plot with the reference"

Dear @zyb1984, Hello, thank you for your feedback. The problem seems to come from the version of reactome.db, which adds "Homo sapiens\r: " to the pathway names in the newest...

bngeneplot() don't support org.Rn.eg.db?

Dear Dong, Thank you for raising the issue, and sending me the e-mail. Could you try again with specifying orgDb=org.Rn.eg.db? For the annotation databases that do not have SYMBOL in...