This repository has been archived by the owner on Jan 24, 2024. It is now read-only.
keep dimensions consistent when removing pathways in netVisual_embeddingPairwise #271
Conversation
This file contains 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
Seems like there's an issue with removing pathways in netVisual_embeddingPairwise. Pathways to be removed are identified in the similarity matrix, where each pathway is represented multiple times (once for each dataset). Each pathway in pathway.remove is labeled according to the dataset in which it meets the removal condition (colSums(similarity)==1) and labeled accordingly (eg "Pathway1--Dataset1"). However, when removing these from each individual dataset's probability matrix, the "--Dataset1" is dropped and "Pathway1" is subsequently removed from all datasets. As a result, the filtered similarity matrix (datasets combined) has a different number of rows compared to the sum of the rows of each dataset's filtered probability matrix. This will happen anytime a pathway is found in multiple datasets but did not meet the removal condition in all of those datasets. I can think of two ways to resolve this: A) remove each pathway in pathway.remove from all datasets (in the similarity matrix and in each individual probability matrix) B) only remove a pathway from an individual dataset's probability matrix if the pathway met the removal condition in that particular dataset I am not too familiar with the theory here, so I'm not sure what is best. For now I've edited the function to do option B, and I labeled the edited portions "edit_1" and "edit_2"
Sign up for free
to subscribe to this conversation on GitHub.
Already have an account?
Sign in.
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Outdated suggestions cannot be applied.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.
in reference to #270