Skip to content

Conversation

pkerpedjiev
Copy link
Member

@pkerpedjiev pkerpedjiev commented Apr 9, 2025

Description

Add doc for chromsizes grid overlay.

Checklist

  • Clear PR title (used for generating release notes).
    • Prefer using prefixes like fix: or feat: to help organize auto-generated
      notes.
  • Unit tests added or updated.
  • Documentation added or updated.

Copy link
Member

@manzt manzt left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Looks good to me. Thanks for documenting.

Only nit is that the ClodiusTileset constructor was intentionally not "public" (not under __all__ for hg.tilesets module), hence why it's not exported at the top level like hg.Tileset (which is the recommended way to make custom tilesets). Public in quotes because everything is a convention in Python.

For now, this is great, but I'm wondering if we could maybe have a more opinionated helper (like the other clodius tilesets) for this use case. What do you think of having a designated chromsizes helper from higlass.tilesets that we could export at the top-level API? E.g.,

import higlass as hg

cs_ts = hg.chromsizes('chromSizes_hg19_reordered.tsv')
cool_ts = hg.cooler("my.multires.cool")

it could also be overloaded to to accept a sequences of chromsizes:

cs_ts = hg.chromsizes([("a", 10_000), ("b", 50_000)])

Let's merge this, and depending on what you think, we could have a separate PR to add such a utility and update the recommended usage.

@pkerpedjiev
Copy link
Member Author

What do you think of having a designated chromsizes helper from higlass.tilesets that we could export at the top-level API?

I'm on board with this. Added a commit adding it to this PR.

it could also be overloaded to to accept a sequences of chromsizes:

I would do this on an as-needed basis.

@manzt manzt merged commit 2819a7a into main Apr 10, 2025
8 checks passed
@manzt manzt deleted the kerpedji/chromsizes-overlay branch April 10, 2025 13:33
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

2 participants