-
Notifications
You must be signed in to change notification settings - Fork 39
Fix color parameter validation in plot_haplotype_network function - Shadow PR #755
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Fix color parameter validation in plot_haplotype_network function - Shadow PR #755
Conversation
…-laarej/malariagen-data-python into fix-plot-haplotype-network-color
…apping case); update tests with assertions; update notebook with examples
|
Check out this pull request on See visual diffs & provide feedback on Jupyter Notebooks. Powered by ReviewNB |
|
Ed and I would need this merged for the Cameroon coluzzii paper. @leehart, do you think you could find the time to review it? |
|
@jonbrenas Why are we introducing the use of This PR also introduces other things to the poetry lock file, e.g. What is the reason for those changes? I'll try to take a closer look at the other code changes later in the week. I'm a bit suspicious about: color="partition" if color is not None else None, |
|
Thanks @leehart. @mohamed-laarej will correct me if I am wrong.
The haplotype networks use
It looks like it was added because of the inclusion of
It looks a little weird but a new column "partition" is created to contain the values that the |
|
Hi @leehart and @jonbrenas , Thanks for reviewing this PR. My memory on the specifics is a bit rusty, but I'll do my best to address your points:
I'm ready to make any necessary adjustments. Thanks again for the review! |
leehart
left a comment
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thanks @jonbrenas @mohamed-laarej . Yep, I reckon we should start using "private" column names, so let's use _partition here. If there are any other simple changes we can make to try to improve the readability here, that would be good too.
leehart
left a comment
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Thanks @mohamed-laarej . Happy with this if @jonbrenas is happy.
|
LGTM. Thanks @mohamed-laarej and @leehart . |
|
@jonbrenas I suspect adding tests to In any case, I suggest that we merge this work in and potentially address migrating these tests (and other work related to #366) in a subsequent issue/PR. For instance, it may be that these tests do actually belong alongside the other tests that are currently in |
Addresses #738.
Shadows #742.
Thanks @mohamed-laarej for the code. I will remove the draft status once I checked I shadowed the PR correctly.