Feeding output from getPerCellTypeDE into Heatmap

[Dimmiso]

HI, Thanks a lot for supporting CONOS! I am back to using this great tool and try now function getPerCellTypeDE. It looks very promising but I cannot find the way how to plot output genes on a heatmap. plotDEheatmap instantly takes as input DE output list from getDifferentialGenes function, but not from getPerCellTypeDE. It is expected as structure of output lists from procedures differs. I tried for plotDEheatmap set de <- NULL and manually feed in top gene list from getPerCellTypeDE via additional.genes parameter. But keeping de <- NULL triggers getDifferentialGenes from inside plotDEheatmap and plotting those genes. Thus, if I am not mistaken there is no simple way to visualize results of getPerCellTypeDE function on heatmap. If I am right, can you please address this issue? It would be ideal to be able feeding output list from getPerCellTypeDE into plotDEheatmap. Thanks a lot! Dmitry

[evanbiederstedt]

Hi @Dimmiso

It might take me some time to get to this properly; please keep emailing me for a fix

That said, it would really help if you can reproducible code I could run to see the problem and fix it.

Thanks, Evan

[Dimmiso]

Hi Evan, thanks a lot for quick answer! in the Rdata file (https://drive.google.com/file/d/1RPPAEntcQ82mX-sSqK4xvVl4-itUA9ei/view?usp=share_link) you will find two objects: de.info.simple - is a output from getDifferentialGenes and de.info is a output from getPerCellTypeDE. The former can be directly used as argument by plotDEheatmap command, but not the latter one. If one compare structure each of the objects with arguments of plotDEheatmap function, it is obvious that output from getPerCellTypeDE cannot be taken as a input. On the other hand plotDEheatmap does not allow plot just external list of genes (only "additional.genes"). I think the simplest solution would be to make it possible to feed it customer gene list to be plotted by the heatmap function. Thanks for your help! Dmitry