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Add function for calculating niches #831

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ca6e7ff
Add function for calculating niches
LLehner May 27, 2024
e08189a
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 27, 2024
1b492ea
Fix pre-commit
LLehner May 27, 2024
032ef90
Fix pre-commit
LLehner May 27, 2024
139819a
Update __init__.py
LLehner May 27, 2024
e0beead
Merge branch 'main' into niche_definitions
LLehner May 27, 2024
a5b810e
Add function
LLehner May 29, 2024
50a8474
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 29, 2024
38c67fb
Update
LLehner Jun 8, 2024
2eb450c
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Jun 8, 2024
86d5efd
adding fide score and jsd metrics
quentinblampey Jun 11, 2024
334b7fb
Add function to test for niche similarity by comparing max (99th perc…
LLehner Jun 11, 2024
54936f9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 11, 2024
2c5cac8
Fix result dataframe
LLehner Jun 11, 2024
6d74f78
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Jun 11, 2024
b5cb056
Add scores to compare different niche calculations
LLehner Jun 11, 2024
2b5ef61
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 11, 2024
c98ec1b
Update doc string and param names
LLehner Jun 11, 2024
9813cf5
Update doc string and param names
LLehner Jun 11, 2024
bb3bdfb
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jun 11, 2024
ebdf1d5
Update neighborhood profile, Remove utag import
LLehner Jun 17, 2024
c6d020b
Fix pre-commit
LLehner Jun 17, 2024
9fa0157
Add utag inner product step
LLehner Jun 17, 2024
49b51ca
Fix output; Remove subsetting, neighborhood options, dimreduction and…
LLehner Jul 10, 2024
d6df534
Update utag output
LLehner Jul 10, 2024
f797ef9
Add cellcharter aggregation step
LLehner Jul 10, 2024
bd16795
Update
LLehner Jul 15, 2024
79c7b52
Fix sparse matrix output
LLehner Jul 16, 2024
9d2104f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jul 16, 2024
5219a30
Fix neighborhood profile calculation
LLehner Jul 16, 2024
8b22409
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Jul 16, 2024
cf5a144
Merge branch 'main' into niche_definitions
timtreis Jul 30, 2024
48ae60b
Merge branch 'main' into niche_definitions
timtreis Aug 21, 2024
dcc542d
Add consensus function
LLehner Aug 26, 2024
2568f7c
Add function to build consensus niche
LLehner Aug 27, 2024
adba136
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Aug 27, 2024
19d4507
Update init
LLehner Aug 27, 2024
5c97651
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 27, 2024
2b47e81
Fix _get_initial_niches
LLehner Aug 27, 2024
3ef2496
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Aug 27, 2024
cf3b51f
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Aug 27, 2024
14ff9a5
Add docstring
LLehner Aug 27, 2024
4457929
Update
LLehner Aug 27, 2024
699b4f0
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Aug 27, 2024
f449d88
some type fixes for mypy
timtreis Aug 30, 2024
dcdd9f6
Update utag
LLehner Oct 1, 2024
12d918c
Merge branch 'main' into niche_definitions
LLehner Oct 1, 2024
6638075
Update neighborhood profile based approach
LLehner Oct 2, 2024
7895bc7
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Oct 2, 2024
ae3b2f8
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 2, 2024
646dbb0
Update doctstring
LLehner Oct 2, 2024
939de0b
Fix
LLehner Oct 2, 2024
c9b4dc5
Update CellCharter approach
LLehner Oct 8, 2024
b1aa25f
Remove commented-out code
LLehner Oct 8, 2024
72d8dc8
Remove draft validation methods
LLehner Oct 8, 2024
4c17024
Merge branch 'main' into niche_definitions
LLehner Oct 8, 2024
a64d0fd
Update init; Fix mypy
LLehner Oct 8, 2024
d682939
Merge branch 'niche_definitions' of https://github.com/scverse/squidp…
LLehner Oct 8, 2024
5bde712
Fix mypy
LLehner Oct 8, 2024
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[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Oct 8, 2024
67a5133
Fix mypy
LLehner Oct 8, 2024
bc38737
Fix mypy
LLehner Oct 8, 2024
342375c
Fix mypy
LLehner Oct 8, 2024
cb4e4d1
Add comments; Remove draft evaluation function
LLehner Oct 9, 2024
e0a67f5
Add tests
LLehner Oct 9, 2024
ae3b4db
Remove unused imports and print statements
LLehner Oct 9, 2024
5a4cfc4
Fix tests
LLehner Oct 9, 2024
3e47df8
Fix test
LLehner Oct 9, 2024
6cbc09e
Fix test
LLehner Oct 10, 2024
6185c0e
Fix test
LLehner Oct 10, 2024
0392fc1
Merge branch 'main' into niche_definitions
LLehner Oct 14, 2024
d4aea2c
Merge branch 'main' into niche_definitions
LLehner Nov 12, 2024
33436bf
Fix sepal
LLehner Nov 12, 2024
37af73d
Merge branch 'main' into niche_definitions
LLehner Nov 18, 2024
ca753a2
Add suggested changes from review
LLehner Nov 30, 2024
e1b2814
Add distance option to neighborhood approach
LLehner Dec 1, 2024
91895cd
Fix docs; Fix relative frequency calculation; Update arg validation f…
LLehner Dec 4, 2024
e771218
Fix tests
LLehner Dec 4, 2024
48d4957
Fix tests
LLehner Dec 4, 2024
0c691a6
Update tests
LLehner Dec 9, 2024
c7ef905
Fix tests
LLehner Dec 9, 2024
87cf01a
Fix tests
LLehner Dec 9, 2024
1a3361b
Fix tests
LLehner Dec 9, 2024
192f146
Fix tests
LLehner Dec 9, 2024
1b41546
Fix tests
LLehner Dec 9, 2024
6dcf561
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Dec 9, 2024
2fc6624
Merge branch 'main' into niche_definitions
LLehner Dec 9, 2024
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1 change: 1 addition & 0 deletions src/squidpy/gr/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
from squidpy.gr._build import mask_graph, spatial_neighbors
from squidpy.gr._ligrec import ligrec
from squidpy.gr._nhood import centrality_scores, interaction_matrix, nhood_enrichment
from squidpy.gr._niche import calculate_niche
from squidpy.gr._ppatterns import co_occurrence, spatial_autocorr
from squidpy.gr._ripley import ripley
from squidpy.gr._sepal import sepal
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