gray nodes (not colored by -log10(value)when creating the map

[veroniquevoisin]

gray nodes (not colored by -log10(value)when creating the map I then modify the fill color style myself. AA was working fine.

[mikekucera]

Hi Veronique, can you please send me the session file. Thanks.

[veroniquevoisin]

Hi, I got a new one today. It is again when I create a new map on a complex session with already a lot of maps (not sure if related).

[veroniquevoisin]

link to session file: https://www.dropbox.com/s/8g5z6v0emckyi9q/test%20_forMike.cys?dl=0

[mikekucera]

Hi Veronique,

In the network above the entire p-value column is zeros. The -log10(pvalue) column is blank. That causes the mapping to not have a range which results in the grey nodes. Is there something wrong with the data, or is this a valid case?

Regardless it should detect when the range is invalid for -log10(pvalue) and use a different mapping.

[veroniquevoisin]

Hi Mike, Yes, it is a valid case. I have an example right now where all the pvalue are 0. They are so many significant pathways that I do a map with the top pathways and GSEA returned them with a pvalue = 0 and -log10(0) = inf. In this case, all nodes should be red and I suppose that you can replace the 0 by any small value? eg 1e-10?

[mikekucera]

Hi Veronique.

When all the pvalues are 0.0 (or missing) then it uses 1e-10 for the pvalue. This results in 10.0 for -log10(pvalue).

This is an example of what the network and style look like when all pvalues are 0.0. Is this ok?

[veroniquevoisin]

Yes, it looks ok