fix: VisiumV1 definition location #165
Closed
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
… updated image in giottoToSeurat
Added spatial_network and nn_network in seuratToGiotto functions plus…
- make generic function `createNetwork()` - new method for all matrices to create sNN and kNN networks. Flexibly allows inclusion of weight, distance cols and name attributes. Allows return as data.table or igraph
Still needs further work aligning all the params and making obvious things to edit in order to get similar behavior to default Giotto operations
…ds info in `convert_to_reduced_spatial_network()`
Add function to calculate euclidean distances for any m x n matrix when provided a data.table of `from` and `to` interactions
Refactors Giotto's spatial and NN networks creation into a hub function that allows starting directly from matrix data. Added tests that currently only ensure parity with original implementation.
Avoids needing to import matrix class definitions.
Try to avoid import of SeuratObject
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Outdated suggestions cannot be applied.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.
No description provided.