Open
Conversation
mnshgl0110
reviewed
Apr 14, 2025
| #ax, c = pltchrbox(ax, agpdata[genome.n][chrgrps[chrs[i]][s]], centrodata[genome.n][chrgrps[chrs[i]][s]], indents[s]-offset, genome.lc, chrwidth, minl=minl) | ||
| ax, c = pltchrbox(ax, v, indents[s] - offset, genome.lc, chrwidth, maxl=chrlength, minl=minl) | ||
| elif itx: | ||
| MCHR = cfg['marginchr'] |
Member
There was a problem hiding this comment.
Currently, the margins are customisable. I dont see how they are being customised within the PR.
Member
|
I assume that the plotsr.py file would also have some changes but that file does not seem to be part of it PR. |
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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
What kind of change does this PR introduce? (Bug fix, feature, docs update, ...)
Implemented four itxalign modes.
Cleaned code, removed redundancies.
Added clarifications to files such as markers.bed.
What is the current behavior? (You can also link to an open issue here)
Users can only plot homologous chromosomes in pairs without a means to visualize interchromosomal structural variations.
What is the new behavior (if this is a feature change)?
Users can plot chromosomes side by side and genomes in pair to visualize interchromosomal structural variations with the new itxalign feature.
Does this PR introduce a breaking change? (What changes might users need to make in their application due to this PR?)
Users do not need to change the command line. However, if they wish to use the itxalign feature other than its default mode, they can do so in the base.cfg or their configuration file.
Other information:
Updated read.me so it is more readable. Reordered paragraphs, paraphrased sentences, and added clarifications. (I will update Tracks & Markers section in the next update.)