Update/peptide intensities - #37
Merged
Merged
Conversation
…rameter Implemented in intensities.py Key results: - Added sample-level row/column faceting. - Preserved facet_by=None behavior. - Kept colors and y-axis consistent across facets. - Forwarded facet_by through proteoform_intensities. - Added explicit validation and ax=True incompatibility.
sparsed matrix handling, layer and ax parameter conventions
Updated intensities.py New contract: ax: Axes | None = None ) -> Axes | list[Axes] Behavior: - Supplied ax is used exactly and returned by identity. - ax=None creates and returns new axes. - Faceted plots return their subplot axes as a list. - facet_by and supplied ax raise ValueError. - Multiple protein_ids with one supplied ax raise ValueError. - Showing or saving does not change the return value.
idf-io
approved these changes
Sep 6, 2026
idf-io
force-pushed
the
update/peptide_intensities
branch
from
September 6, 2026 23:40
e544953 to
c1a3c8b
Compare
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Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be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.
updated: proteoform_intensities, peptide_intensities with facet_by parameter
Implemented in intensities.py
Key results:
updated: AGENTS.md
sparsed matrix handling, layer and ax parameter conventions
updated: peptide_intensities ax parameter
Updated intensities.py
New contract:
ax: Axes | None = None
) -> Axes | list[Axes]
Behavior: