Repository navigation
Conversation
Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>
There was a problem hiding this comment.
🟡 Changes recommended
Merge tie-breaking and dendrogram orientation need explicit conventions to produce reproducible results across implementations.
2 open issues
What changed in this PR
Adds a reusable Ward-linkage protocol for clustering and displaying signature similarity matrices.
Changes:
- Defines matrix and Ward-compatible distance prerequisites.
- Describes clustering, annotated heatmaps, and provenance recording.
- Preserves similarity values and excludes preprocessing.
| File | Description |
|---|---|
| protocols/ward-linkage-signature-matrix-clustering/protocol.md | Adds the clustering protocol, input requirements, outputs, and interpretation limits. |
Review effort: Balanced
Comment on lines
+76
to
+78
| Use a deterministic tie rule and record it when two candidate merges have the | ||
| same objective increase. Record the linkage method, distance representation, | ||
| tie rule, merge sequence or dendrogram, and any software and version used. |
Comment on lines
+87
to
+90
| Use the leaf order of the Ward dendrogram to order both rows and columns of | ||
| the original similarity matrix. Apply the identical order to every annotation | ||
| track. Do not replace the similarity values with distances or reorder rows | ||
| and columns independently. |
…rule Take the similarity-to-distance conversion (1 - s) into this protocol as issue waldronlab#9 specifies, state that the Ward criterion is applied to squared distances (ward.D2, not ward.D), give the Lance-Williams update, define the default tie rule by input index, and require the leaf order to be recorded. Drafted with Claude Code.
Drafted with Claude Code.
lwaldron
approved these changes
Oct 18, 2026
Drafted with Claude Code.
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
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.
Adds the Ward-linkage signature similarity matrix clustering protocol.
The protocol:
Closes #9