Add ability to adjust alpha, min alignment length, color scheme and option to diagonalize synteny plots #5195
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
|
these features can greatly enhance complex synteny plot readability before after |
|
currently uses globalAlpha for the opacity but might want to use per-line alpha as globalOpacity is canvas specific |
cmdcolin
force-pushed
the
adjust_alpha
branch
from
006471c to
534257a
Compare
cmdcolin
force-pushed
the
adjust_alpha
branch
3 times, most recently
from
c6b3f4c to
11092eb
Compare
cmdcolin
force-pushed
the
adjust_alpha
branch
from
11092eb to
4eb8f2f
Compare
cmdcolin
force-pushed
the
adjust_alpha
branch
from
10c296e to
6d5bd34
Compare
cmdcolin
force-pushed
the
adjust_alpha
branch
from
6d5bd34 to
cde094d
Compare
|
Example of coloring by query sequence with a mild alpha-transparency and diagonalized entries 
comparing to our 'before pic' this is much better 
|
cmdcolin
changed the title
This was referenced Nov 5, 2025
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes #2110
Fixes #4424
This adapts code from https://jmonlong.github.io/Hippocamplus/2017/09/19/mummerplots-with-ggplot2/ (also added to dotplot view) to 'diagonalize' or reorder chromosomes in the synteny view
Also adds alpha transparency/opacity slider and min length sliders and some color options like color by query