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microbiome
Simplify heatmap examples
Hi!
Currently, the visualisation chapter shows heatmap examples with multiple packages (pheatmap, sechm and ggplot). These examples require a great deal of manual manipulation of the generated graphics to resize and combine them into a nice plot. However, virtually all the heatmaps in these examples can be generated with ComplexHeatmap in a simpler way. Thus, I propose to convert the current examples to use ComplexHeatmap instead.
Additionally, there could be a short comparison between ComplexHeatmap, suitable for hierarchical clustering, and sechm, suitable for rows ordered by the angles of an MDS plot (check issue #146).
I have streamlined and polished a little bit the code of the examples, but if anyone else is interested, they can carry on this work by forking or directly pushing to the ribo branch.
Seems good to me! There can be educational value with the ggplot examples, can we leave them at the end of the Quarto document as hidden, non-evaluated chunks not shown in the book?
Sorry for the long delay! I think this PR is now outdated since the current devel has developed further. Maybe I'll reopen it in the future.
Oh, ok. I hope that not too much good work on this went abandoned! Let's try to deal with ongoing PRs efficiently always, otherwise this may happen indeed.