No colorcode in the KEGG figure

[Elseedy28]

Hello,
may be i have wrong input data or code as i am new in pathview , i attached you the file iam using and the code i am using is
Data <- read.delim("KEGG IPonly2.csv", sep = ";", header = TRUE)
pv.out <- pathview(gene.data = Data[, 1], pathway.id = "04010",
species = "hsa", out.suffix = "Data1",kegg.native = TRUE)

and the end product usually two figure with no color map for my input genes, so idon't know if it because of i have bad input or code
i tried also the Gaphiz view and i have the same problem

Thanks

KEGG IPonly2.csv

[howtofindme]

Hello, may be i have wrong input data or code as i am new in pathview , i attached you the file iam using and the code i am using is Data <- read.delim("KEGG IPonly2.csv", sep = ";", header = TRUE) pv.out <- pathview(gene.data = Data[, 1], pathway.id = "04010", species = "hsa", out.suffix = "Data1",kegg.native = TRUE)

and the end product usually two figure with no color map for my input genes, so idon't know if it because of i have bad input or code i tried also the Gaphiz view and i have the same problem

Thanks

KEGG IPonly2.csv

same problem, have you solved it and how? thanks

[Elseedy28]

No i didn't solve it till now I hope that there is asolution as i would like to publish these data Le ven. 21 juil. 2023 à 09:23, youngleel ***@***.***> a écrit :

…

Hello, may be i have wrong input data or code as i am new in pathview , i attached you the file iam using and the code i am using is Data <- read.delim("KEGG IPonly2.csv", sep = ";", header = TRUE) pv.out <- pathview(gene.data = Data[, 1], pathway.id = "04010", species = "hsa", out.suffix = "Data1",kegg.native = TRUE) and the end product usually two figure with no color map for my input genes, so idon't know if it because of i have bad input or code i tried also the Gaphiz view and i have the same problem Thanks KEGG IPonly2.csv <https://github.com/datapplab/pathview/files/9765357/KEGG.IPonly2.csv> same problem, have you solved it and how? thanks — Reply to this email directly, view it on GitHub <#22 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A3RUBCLVCIQWC4CTURQ7IETXRIU7TANCNFSM6AAAAAARDJXUCM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[raw937]

Are you still having this issue?

If you have the same issues place in:
https://github.com/Kannapolis-Bioinformatics/pathview/issues

We can answer your question

many thanks,
Rick

[raw937]

You current input ia not KOs. I believe they are geneIDs. What gave you this output?

[raw937]

Gage/pathview need KOs
You can use metacerberus at
www.github.com/raw-lab/metacerberus