elkebir-group / cnaviz Goto Github PK

It would be more convenient if the scatter plot could also show the estimated (closest) copy number states (major and minor copy number) next to the centroids.
I'm thinking of something similar to the below:

1. The error message is:

   Traceback (most recent call last):
     File "/home/chuanyi5/program/cnaviz/scripts/segment_bins.py", line 18, in <module>
       segments = segmentBins(bb=combo, clusters=clusters, samples=samples)
   NameError: name 'segmentBins' is not defined

   I think it's caused by segmentBins is no longer defined in cluster_bins, since cluster_bins was renamed to cluster_bins_gmm after v1.0.1. Changing the import to from hatchet.utils.cluster_bins_gmm import * solves the problem.
2. This script always read the same input file. It would be better to use argparse.

Some browsers (I tried Firefox) will download the log file only, which is insufficient to recover the manual operations made using CNAViz. This may have to do with behavior around multiple downloads from the same trigger.

Easy fix could be to add a drop-down menu or another export button.

In order to accommodate variable length bins in HATCHet v1.0+, and make linear plots look better when users zoom in and the bin sizes are large (such as 500kb), is it better to draw line segments instead of dots in linear plots?

Since read counts can be skewed around centromeres, is it possible to differentiate/dim/hide bins around them?
I know that HATCHet already takes care of centromeres when counting reads (HATCHet).