How to make chromVAR plot?

Question

[Chris]

Hi all,

I found an interesting plot in a paper using the tool name chromVAR.
https://www.cell.com/cell-reports/pdf/S2211-1247(19)30666-7.pdf.
However I could not find the code in the Github page of the paper.
https://github.com/sankaranlab/erythroid-profiling Do you know how to make a plot like this from ATAC seq data? Thank you so much!

[MatthewP]

This is heatmap/plot which can plot by ComplexHeatmap. You need to prepare your (chromVAR)data to a matrix, then plot the heatmap.

[Chris]

Thank you so much for sharing! Would you please explain why they used chromVAR in the legend? I thought the plot use a function in chromVAR tool?

[ATpoint]

chromVAR can calculate deviation scores but has no plotting routines. This is simply deviation/variability Z scores between samples in a heatmap. No magic here. https://github.com/sankaranlab/erythroid-profiling/blob/master/code/atac/07a_chromVAR_EryOnly.R#L68

[Chris]

Thank you so much! I appreciate it.

[Chris]

Would you please confirm the function to make this plot?

Seem it is plotVariability()