It would be great to be able to click on a cell in the matrix and view the underlying data in a new figure.
metaseq already has the infrastructure needed to do this.
I read through the metaseq codebase to see what it would take to factor that stuff out into another, possibly simplified package.
Turns out it's not trivial. The signal plotting is actually a really big part of metaseq. It supports plotting bigBed, bigWig, BAM, and all the bedtools formats via a uniform API, along with a flexible way to create customized mini-browsers. But to do all this, it has a lot of dependencies (Cython, HTSeq, pysam, bx-python, gffutils). These are all easy_install-able, so hopefully it won't be that much of an issue if scurgen imports it.
I can prototype something for the scurgen mpl GUI that imports metaseq, and I guess you can see if it's worth it to require all those other packages.
It would be great to be able to click on a cell in the matrix and view the underlying data in a new figure.
metaseq already has the infrastructure needed to do this.
I read through the metaseq codebase to see what it would take to factor that stuff out into another, possibly simplified package.
Turns out it's not trivial. The signal plotting is actually a really big part of metaseq. It supports plotting bigBed, bigWig, BAM, and all the bedtools formats via a uniform API, along with a flexible way to create customized mini-browsers. But to do all this, it has a lot of dependencies (Cython, HTSeq, pysam, bx-python, gffutils). These are all
easy_install-able, so hopefully it won't be that much of an issue if scurgen imports it.I can prototype something for the scurgen mpl GUI that imports metaseq, and I guess you can see if it's worth it to require all those other packages.