cellTopicHeatmap - annotations about cistopic

[cbravo93]

Hi @cmuus !

I normally use RStudio or save to pdf/png (with default parameters), and it displays ok (with ComplexHeatmap v1.17.1). However, updating to the latest version of ComplexHeatmap (in Bioconductor, v2.0.0) gives this (I guess this is what you see right?)

Changing the following:

annotation <- ComplexHeatmap::HeatmapAnnotation(df = object.cell.data[,colorBy,drop=FALSE], col = colVars, which='column', width = unit(5, "mm"))

by:

annotation <- ComplexHeatmap::HeatmapAnnotation(df = object.cell.data[,colorBy,drop=FALSE], col = colVars, which='column')

seems to give the proper output:

Did this solve the problem for you? I will make updates on the function so it works properly with any of the versions.

An alternative option to customise better your heatmap is to extract the cell-topic matrix using the function modelMatSelection().

Thanks a ton for reporting!

C

[cmuus]

Thank you for looking into it so quickly @cbravo93! This is all in line with what I see, sorry I didn't post example plots. You might want to specify height? Thanks for the modelMatSelection() hint, that's exactly what I ended up doing. I also just modified cellTopicHeatmap to output the heatmap and annotation objects. It might be too much to include in the main branch, but maybe you could include a flag that, when true, allows the user to output a tuple with heatmap and annotation?

[yanwengong]

@cmuus @cbravo93
I am trying to modify the arrange of cells showing on the cisTopic heatmap. Instead of having the figure below, I would like the cells arranged by my legends. Just as @cbravo93 's plot!

I couldn't find a way to do it with cisTopic vignette. I wonder how you guys make it. Do you mind share the code or direct me to the right source?

Thanks in advance for your help.