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tanaylab / mcATAC

Metacell analysis for ATAC data
https://tanaylab.github.io/mcATAC/
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Feat@tracks class #50

Closed aviezerl closed 2 years ago

aviezerl commented 2 years ago

Added a new class McTracks which holds the ATAC tracks, and create a cleaner OOP model where all objects inherit from a virtual class called ATAC. This would allow us to attach RNA data / metadata to both peaks,tracks and counts objects. While doing that I renamed McATAC/ScATAC to McPeaks/ScPeaks, so - many files where changed.

In addition, I added a mechanism to extract and cache a matrix from the ATAC tracks + a downsampled version.

Still missing - integrating the plotting of these matrices, peak detection, vignette entries, and, of course, more comprehensive tests.

aviezerl commented 2 years ago

@yonatans2, would it be OK to merge? Do you want to do another pass?

I know it is far from complete but I don't want the master branch to diverge too much, especially since Roni is already using it.

We currently have two functions to plot genomic regions, and we need to unify them, hopefully with the ComplexHeatmap infrastructure you created. What stopped me from doing it was that I didn't find a way to efficiently plot the DAC detector mask above the current plot, but I am sure it is solvable.