getSpatialParametersExternal #37
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
…nd transfoming the SpaceMarkersMetric with log2(abs()+1) to prevent skewing of the scale.Updated Package version.
…ders the spatial pattern itself in calculating influence instead of only considering the spots around it
…ders the spatial pattern itself in calculating influence instead of only considering the spots around it. Updated default kernelthreshold to be slightly more stringent since more hotspots will be produced. Updated Package version
…ecify sigma for kernel width for smoothing and outlier threshold for hotspots. The default behavior is to pull the spot diameter from a 10xVisium .json file from the usual spatial folder created by Visium.Updated version number
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Outdated suggestions cannot be applied.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.
Added a getSpatialParametersExternal function to allow the user to specify sigma for kernel width for smoothing and outlier threshold for hotspots. The default behavior is to pull the spot diameter from a 10xVisium .json file from the usual spatial folder created by Visium. Updated version number