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Fix neighborhood matrix indexing due to subsetting #824

Merged
merged 8 commits into from
Nov 23, 2022
Merged

Fix neighborhood matrix indexing due to subsetting #824

merged 8 commits into from
Nov 23, 2022

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alex-l-kong
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What is the purpose of this PR?

Closes #822. Patches an issue where passing a subsetted all_data in create_neighborhood_matrix causes indexing errors when using the index for cell_neighbor_counts and cell_neighbor_freqs.

How did you implement your changes

Call reset_index on all_neighborhood_data after subsetting the columns on all_data.

@alex-l-kong alex-l-kong self-assigned this Nov 11, 2022
@alex-l-kong alex-l-kong marked this pull request as draft November 11, 2022 03:44
@alex-l-kong alex-l-kong marked this pull request as ready for review November 22, 2022 21:58
@alex-l-kong
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New indexing has been tested on the neighborhood analysis notebook, doesn't throw errors even if a non-continuous 0-based index is passed.

ngreenwald
ngreenwald approved these changes Nov 23, 2022
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Looks good

@ngreenwald ngreenwald merged commit 1b2183c into main Nov 23, 2022
@ngreenwald ngreenwald deleted the neigh_index branch November 23, 2022 05:19
@srivarra srivarra added the bug Something isn't working label Jan 10, 2023
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@ngreenwald ngreenwald ngreenwald approved these changes

@cliu72 cliu72 Awaiting requested review from cliu72

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@alex-l-kong alex-l-kong

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create_neighborhood_matrix assumes continuous index in cell table
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@alex-l-kong @ngreenwald @srivarra