Heatmap tools in SEtools package

[antagomir]

The SEtools package provides SE integration for pheatmap and ComplexHeatmap packages, see the vignette.

Consider whether this would be useful to update/improve the current heatmap plotting examples in OMA. They rely on the same packages but this seems to provide added capabilities for SE objects.

Also includes the do.scale argument to scale heatmap rows, which correspond to the Z transformation that we so far did as a separate step for heatmaps.

[TuomasBorman]

SEtools::sechm is deprecated, they have moved sechm into sechm package

I added example here
PR: #116

I'm wondering if we should have one chapter dedicated to visualization that have all these general tricks for heatmap, boxplot, jitterplot and so on. Now these heatmap examples are under community composition.

[antagomir]

There could be a dedicated chapter on visualization, collecting key tricks in one place. Also: we can actively cite the other resources and avoid too much duplication in examples. While keeping OMA relatively self-contained.

But I would not entirely remove the examples from other chapters, either, because visualization is an important tool to understand the data also in those other chapters.

sechm package seems useful!

[TuomasBorman]

That's true. Currently, that heatmap example is quite long and it includes additional stuff (how to do complex hetamap with ggplot2 alone...), so that kind of tricks could have own chapter

[antagomir]

To do.