search

etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
782 stars 212 forks source link

Wrong background colors for linked alignment #575

Closed Just08 closed 2 years ago

Just08 commented 3 years ago

Hi,

I don't understand why my nucleotide linked alignment appears in yellow , orange , grey and light grey instead of the default colors in faces.py https://github.com/etetoolkit/ete/blob/master/ete3/treeview/faces.py#L140 .

First, I was thinking the problem was that my sequences contain N character, but whenever I had a 'N' key in faces. _ntbgcolors dictionary or replaces N by spaces in my sequences, linked alignment still have the inappropriate colors.

How can I have default colors work for my linked alignment?

Thanks in advance

jhcepas commented 2 years ago

as you notived, these are hardcoded in the treeview.faces module. You can, however, import faces.py, change the bg-colors dict and it will be used for the subsequent visualizations.

Yogesh1-11 commented 8 months ago

hi how to access the columns of alignment for recolouring?