Question about the red and green colors on the KEGG pictures

[powerhorse1986]

Hi, I am analyzing a lung cancer dataset using pathfindR. It's awesome. Just have two questions about how to interpret the png pics from KEGG.

1. Does a red colored node mean a gene being upregulated and a green colored node mean a gene being downregulated?
2. If the answer to question 1 is yes, then how to explain that some genes in the enriched_terms.html file being classifed as upregulated but they are green colored in the KEGG png pic?
   That's all my question. Thanks so much.

[egeulgen]

Hello,

There was a bug in the coloring portion of the visualization function, which I've just fixed. You may download the latest development version which contains the fixed function:

install.packages("devtools") # if you have not installed "devtools" 
devtools::install_github("egeulgen/pathfindR")

[powerhorse1986]

Hi,

I just tried the latest version, but the plots were still the same.

[egeulgen]

Can you share output of sesssionInfo()

…

-E

On 9 Nov 2021, at 19:52, powerhorse1986 ***@***.***> wrote:  Hi, I just tried the latest version, but the plots were still the same. — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android.

[egeulgen]

do you mind sharing the data you use (the input data and the pathfindR output)? you can email me at egeulgen [at] gmail.com

[powerhorse1986]

Hi Ulgen,

I have to ask my boss. Because this dataset came from a real patient.

[powerhorse1986]

Do you mind I sending you the enriched_terms.html and the colored KEGG plot for p53 to you first?

[egeulgen]

that would only help me verify that the issue still persists but I wouldn't be able to debug it

[powerhorse1986]

Hi Ulgen, I just sent a mock data set to you. Please check your mailbox. Thanks.