Code

Release 0.19.0#203

Code

Merged

ambarrio merged 128 commits intomainPixelgenTechnologies/pixelator:mainfrom devPixelgenTechnologies/pixelator:devCopy head branch name to clipboardDec 10, 2024

+3,830-2,579

Commits

Commits on Aug 20, 2024

• Fix some typos in the human-readable assay region names

  fbdtemme

  committed
  1297a72

  Copy full SHA for 1297a72

• Only install dev packages in dev container layer

  fbdtemme

  committed
  5dcad08

  Copy full SHA for 5dcad08

• Merge pull request #180 from PixelgenTechnologies/misc-small-fixes

  Show description for 622cb6f
  fbdtemme

  authored
  622cb6f

  Copy full SHA for 622cb6f

Commits on Aug 21, 2024

• Added abundance_colocalization_plot function

  ptajvar

  committed
  dd98043

  Copy full SHA for dd98043

• added test for abundance_colocalization_plot

  ptajvar

  committed
  0aefc35

  Copy full SHA for 0aefc35

Commits on Aug 22, 2024

• added plot legend explanation for abundance_colocalization_plot

  ptajvar

  committed
  a4ab4dd

  Copy full SHA for a4ab4dd

• updated CHANGELOG.md

  ptajvar

  committed
  334d78c

  Copy full SHA for 334d78c

• Fix tox and modernize tests.yml worfklow

  fbdtemme

  committed
  4b96a62

  Copy full SHA for 4b96a62

• Merge pull request #179 from PixelgenTechnologies/feature/exe-1852-scatterplot-abundance-colocalization

  Show description for 9e1afbd
  ptajvar

  authored
  9e1afbd

  Copy full SHA for 9e1afbd

• Remove leftover workflow step

  fbdtemme

  committed
  03baf4a

  Copy full SHA for 03baf4a

• Silence a typing warning

  fbdtemme

  committed
  1299abe

  Copy full SHA for 1299abe

Commits on Aug 23, 2024

• Merge pull request #184 from PixelgenTechnologies/fix-tox

  Show description for 9d624d0
  fbdtemme

  authored
  9d624d0

  Copy full SHA for 9d624d0

• Rename single-cell command to single-cell-mpx and make it an alias

  fbdtemme

  committed
  1963fa8

  Copy full SHA for 1963fa8

• Update workdir and cli info to deal with both single-cell-mpx and single-cell

  fbdtemme

  committed
  911c222

  Copy full SHA for 911c222

• Update tests

  fbdtemme

  committed
  1d2010e

  Copy full SHA for 1d2010e

• Update CHANGELOG.md

  fbdtemme

  committed
  0c17c13

  Copy full SHA for 0c17c13

• Fix typos snipped -> snippet

  fbdtemme

  committed
  235d84f

  Copy full SHA for 235d84f

• Remove unused import

  fbdtemme

  committed
  1fe31df

  Copy full SHA for 1fe31df

• Fix a typo in CLIInvocationInfo.get_option

  fbdtemme

  committed
  effa856

  Copy full SHA for effa856

• Revert single-cell-mpx entrypoint renaming

  fbdtemme

  committed
  59744e1

  Copy full SHA for 59744e1

• Revert CHANGELOG change

  fbdtemme

  committed
  e2b4679

  Copy full SHA for e2b4679

• Revert testdata update

  fbdtemme

  committed
  88657ac

  Copy full SHA for 88657ac

• Merge pull request #182 from PixelgenTechnologies/feature/exe-1954

  Show description for 6b21513
  fbdtemme

  authored
  6b21513

  Copy full SHA for 6b21513

Commits on Aug 27, 2024

• add support for multiple targets in get_differential_colocalization

  ptajvar

  committed
  36b6002

  Copy full SHA for 36b6002

• added support for multiple targets in plot_colocalization_diff_heatmap

  ptajvar

  committed
  51c025e

  Copy full SHA for 51c025e

• fixed output type for plot_colocalization_diff_heatmap

  ptajvar

  committed
  7dfd750

  Copy full SHA for 7dfd750

• updated colocalization heatmap and volcano plots

  ptajvar

  committed
  f14729b

  Copy full SHA for f14729b

• fix: replaced p_adj and target columns in test_get_differential_colocalizaiton

  ptajvar

  committed
  28b6daf

  Copy full SHA for 28b6daf

• added plot titles to differential colocalization volcano plots

  ptajvar

  committed
  94a908e

  Copy full SHA for 94a908e

• updated CHANGELOG.md

  ptajvar

  committed
  3d1fd36

  Copy full SHA for 3d1fd36

• use_z_score is replaced by value_column in colocalization plot functions to allow for more flexibility in the input data.

  ptajvar

  committed
  d9fa121

  Copy full SHA for d9fa121

• added plot_polarity_diff_volcano

  ptajvar

  committed
  86372e2

  Copy full SHA for 86372e2

• Merge pull request #183 from PixelgenTechnologies/feature/exe-1935-support-multi-target-differential-colocalization

  Show description for 68074e6
  ptajvar

  authored
  68074e6

  Copy full SHA for 68074e6

• Merge pull request #185 from PixelgenTechnologies/feature/exe-1936-add-differential-polarity-plot

  Show description for 50261bb
  ptajvar

  authored
  50261bb

  Copy full SHA for 50261bb

Commits on Aug 30, 2024

• Updated probability distance calculations

  ludvigla

  committed
  4b7b687

  Copy full SHA for 4b7b687

• Added test for multigraph

  ludvigla

  committed
  ddb36a9

  Copy full SHA for ddb36a9

• updated CHANGELOG

  ludvigla

  committed
  e097b1f

  Copy full SHA for e097b1f

• Fixed typo

  ludvigla

  committed
  8bbabb5

  Copy full SHA for 8bbabb5

Commits on Sep 2, 2024

• skip casting nodes and edges to list

  ptajvar

  committed
  c9baf9b

  Copy full SHA for c9baf9b

• Merge pull request #186 from PixelgenTechnologies/exe-1997-improve-wpmds

  Show description for 8d05475
  ptajvar

  authored
  8d05475

  Copy full SHA for 8d05475

Commits on Sep 10, 2024

• Relax pyarrow dependency to >=14

  fbdtemme

  committed
  805f2e7

  Copy full SHA for 805f2e7

• Merge pull request #187 from PixelgenTechnologies/update-pyarrow

  Show description for 8526c31
  fbdtemme

  authored
  8526c31

  Copy full SHA for 8526c31

Commits on Sep 16, 2024

• fix: multi-target polarity plot

  ptajvar

  committed
  ed0d201

  Copy full SHA for ed0d201

• Merge pull request #189 from PixelgenTechnologies/feature/exe-2009-fix-multi-target-polarity

  Show description for 848fa42
  ptajvar

  authored
  848fa42

  Copy full SHA for 848fa42

Commits on Sep 17, 2024

• midway

  ptajvar

  committed
  6e46177

  Copy full SHA for 6e46177

• midway2

  ptajvar

  committed
  7c8fa9f

  Copy full SHA for 7c8fa9f

• midway

  ptajvar

  committed
  8a2fbe3

  Copy full SHA for 8a2fbe3

• added xxhash to dependencies

  ptajvar

  committed
  1629fbc

  Copy full SHA for 1629fbc

• updated poetry.lock

  ptajvar

  committed
  b814b6e

  Copy full SHA for b814b6e

• revert poetry.lock

  ptajvar

  committed
  60765db

  Copy full SHA for 60765db

• revert poetry.lock

  ptajvar

  committed
  7534a09

  Copy full SHA for 7534a09

• fix: typo

  ptajvar

  committed
  3c8c4ca

  Copy full SHA for 3c8c4ca

• updated poetry.lock

  ptajvar

  committed
  5c1deb2

  Copy full SHA for 5c1deb2

• adapting tests

  ptajvar

  committed
  6e68c29

  Copy full SHA for 6e68c29

• make regular expression match compatible with python 3.10

  ptajvar

  committed
  075b4d8

  Copy full SHA for 075b4d8

• fix: split_remaining_and_removed_edgelist output type in graph utils

  ptajvar

  committed
  828da76

  Copy full SHA for 828da76

• add LEIDEN_RESOLUTION as a constant parameter

  ptajvar

  committed
  19dd958

  Copy full SHA for 19dd958

• improve map_upis_to_components speed

  ptajvar

  committed
  bd36169

  Copy full SHA for bd36169

• rerun plot tests

  ptajvar

  committed
  744aa90

  Copy full SHA for 744aa90

• applied suggestions from pull request review

  ptajvar

  committed
  50747f0

  Copy full SHA for 50747f0

Commits on Sep 20, 2024

• using pandas edges instead of polars for improved speed in recover_technical_multiplets

  ptajvar

  committed
  6496116

  Copy full SHA for 6496116

Commits on Sep 24, 2024

• doing 5 trials for each leiden run

  ptajvar

  committed
  bcde2c0

  Copy full SHA for bcde2c0

• lower leiden resolution to 0.01 and increase the community rejoin threshold to 20

  ptajvar

  committed
  2eec02b

  Copy full SHA for 2eec02b

• fix: added back graph report generation

  ptajvar

  committed
  43250d5

  Copy full SHA for 43250d5

Commits on Sep 25, 2024

• Update src/pixelator/graph/community_detection.py

  Show description for fa18bfb
  

  ptajvar

  and

  ambarrio

  authored
  fa18bfb

  Copy full SHA for fa18bfb

• Update src/pixelator/graph/community_detection.py

  Show description for 5a3a175
  

  ptajvar

  and

  ambarrio

  authored
  5a3a175

  Copy full SHA for 5a3a175

• Update src/pixelator/graph/community_detection.py

  Show description for c1c2b68
  

  ptajvar

  and

  ambarrio

  authored
  c1c2b68

  Copy full SHA for c1c2b68

Commits on Sep 26, 2024

• Applied the review comments

  ptajvar

  committed
  4c372af

  Copy full SHA for 4c372af

Commits on Sep 30, 2024

• removing components_modularity from edgelist_metrics

  ptajvar

  committed
  ed74a2d

  Copy full SHA for ed74a2d

Commits on Oct 1, 2024

• Merge pull request #192 from PixelgenTechnologies/feature/exe-2015-edgelist-metrics-light

  Show description for e3e2c06
  ptajvar

  authored
  e3e2c06

  Copy full SHA for e3e2c06

• fix: format

  ptajvar

  committed
  14086e4

  Copy full SHA for 14086e4

• reducing STRONG_EDGE_THRESHOLD to 5

  ptajvar

  committed
  6884aa9

  Copy full SHA for 6884aa9

• stub clarification

  ptajvar

  committed
  a2e3bf9

  Copy full SHA for a2e3bf9

• Update src/pixelator/graph/community_detection.py

  Show description for a477cba
  

  ptajvar

  and

  ambarrio

  authored
  a477cba

  Copy full SHA for a477cba

• adding number of edges with colliding UPIs to graph report.json

  ptajvar

  committed
  d0ff1d9

  Copy full SHA for d0ff1d9

Commits on Oct 2, 2024

• update CHANGELOG.md

  ptajvar

  committed
  62b7cbc

  Copy full SHA for 62b7cbc

• replaced the constant STRONG_EDGE_THRESHOLD with --max-edges-to-split as an input to the graph step cli.

  ptajvar

  committed
  5b4df56

  Copy full SHA for 5b4df56

• Merge pull request #188 from PixelgenTechnologies/feature/exe-1989-iterative-leiden

  Show description for 2a43b72
  ptajvar

  authored
  2a43b72

  Copy full SHA for 2a43b72

Commits on Oct 18, 2024

• Update fspec, and update lock file

  johandahlberg

  committed
  cad67e3

  Copy full SHA for cad67e3

• Merge pull request #194 from PixelgenTechnologies/chore/update-fsspec

  Show description for 9246b33
  johandahlberg

  authored
  9246b33

  Copy full SHA for 9246b33

Commits on Oct 20, 2024

• fix: changelog merge conflict

  ambarrio

  committed
  a2d0fed

  Copy full SHA for a2d0fed

Commits on Oct 21, 2024

• adding annotation of potential doublets

  ptajvar

  committed
  8ad1a9b

  Copy full SHA for 8ad1a9b

• split _compute_sub_communities from _assess_doublet

  ptajvar

  committed
  e08516d

  Copy full SHA for e08516d

• Added n_edges_to_split_potential_doublets

  ptajvar

  committed
  128f116

  Copy full SHA for 128f116

• Reduced Leiden resolution by 0.5 in the annotation step

  ptajvar

  committed
  42b1537

  Copy full SHA for 42b1537

• updated CHANGELOG.md

  ptajvar

  committed
  7a3e5c1

  Copy full SHA for 7a3e5c1

• fix: set default values for fraction_potential_doublets and n_edges_to_split_potential_doublets

  ptajvar

  committed
  2b03001

  Copy full SHA for 2b03001

• fix: make fraction_potential_doublets non-optional

  ptajvar

  committed
  4d38f39

  Copy full SHA for 4d38f39

Commits on Oct 22, 2024

• Update src/pixelator/pixeldataset/utils.py

  Show description for 13f6618
  

  ptajvar

  and

  johandahlberg

  authored
  13f6618

  Copy full SHA for 13f6618

• Update src/pixelator/pixeldataset/utils.py

  Show description for a427c36
  

  ptajvar

  and

  johandahlberg

  authored
  a427c36

  Copy full SHA for a427c36

• Update src/pixelator/pixeldataset/utils.py

  Show description for 19bd66a
  

  ptajvar

  and

  johandahlberg

  authored
  19bd66a

  Copy full SHA for 19bd66a

• Update src/pixelator/pixeldataset/utils.py

  Show description for 2e46451
  

  ptajvar

  and

  johandahlberg

  authored
  2e46451

  Copy full SHA for 2e46451

• fix: typo

  ptajvar

  committed
  8db21e2

  Copy full SHA for 8db21e2

• added RELATIVE_ANNOTATE_RESOLUTION as a constant

  ptajvar

  committed
  98da20f

  Copy full SHA for 98da20f

• make fraction_potential_doublets and n_edges_to_split_potential_doublets optional

  ptajvar

  committed
  69041e7

  Copy full SHA for 69041e7

• set default fraction_potential_doublets and n_edges_to_split_potential_doublets to None

  ptajvar

  committed
  63b4ef1

  Copy full SHA for 63b4ef1

• explicitly check n_edges_to_split_doublet exists before using sum

  ptajvar

  committed
  fb156c9

  Copy full SHA for fb156c9

• fix: typecheck

  ptajvar

  committed
  7042c1f

  Copy full SHA for 7042c1f

• Merge pull request #193 from PixelgenTechnologies/feature/exe-2025-annotate-potential-doublets

  Show description for 7ca7168
  ptajvar

  authored
  7ca7168

  Copy full SHA for 7ca7168

• Add "depth" column to the discarded_edgelist

  ptajvar

  committed
  436867f

  Copy full SHA for 436867f

• updated CHANGELOG.md

  ptajvar

  committed
  3d4cc74

  Copy full SHA for 3d4cc74

• Added multiplet recovery metrics to graph stage's report.json

  ptajvar

  committed
  b63fb91

  Copy full SHA for b63fb91

• fix: typecheck

  ptajvar

  committed
  dde6fbe

  Copy full SHA for dde6fbe

• fix: Typechek

  ptajvar

  committed
  37d1ddf

  Copy full SHA for 37d1ddf

• casting report parameters to corresponding data types

  ptajvar

  committed
  63145f7

  Copy full SHA for 63145f7

• Merge pull request #195 from PixelgenTechnologies/feature/exe-2046-add-depth-info-to-discarded-edgelist

  Show description for ffa1b8d
  ptajvar

  authored
  ffa1b8d

  Copy full SHA for ffa1b8d

Commits on Oct 28, 2024

• Do dynamic imports of graspologic for performance

  johandahlberg

  committed
  3027643

  Copy full SHA for 3027643

• Merge pull request #196 from PixelgenTechnologies/chore/dynamic-import-of-graspologic

  Show description for d9e4022
  johandahlberg

  authored
  d9e4022

  Copy full SHA for d9e4022

Commits on Nov 5, 2024

• casting component to string before checking for match when constructing a graph from a pixel object.

  ptajvar

  committed
  dbfbd98

  Copy full SHA for dbfbd98

Commits on Nov 6, 2024

• Merge pull request #197 from PixelgenTechnologies/fix/exe-2058-graph-error-for-missing-component

  Show description for 9834f48
  ptajvar

  authored
  9834f48

  Copy full SHA for 9834f48

Commits on Nov 13, 2024

• Enforce more nodes than dimensions for pmds

  johandahlberg

  committed
  56322c8

  Copy full SHA for 56322c8

• Add test

  johandahlberg

  committed
  112b41c

  Copy full SHA for 112b41c

• Update changelog

  johandahlberg

  committed
  b25a7ec

  Copy full SHA for b25a7ec

• Exit with status 1 if less 50% of reads demuxed

  johandahlberg

  committed
  5d1bd31

  Copy full SHA for 5d1bd31

• Update changelog

  johandahlberg

  committed
  d3172c6

  Copy full SHA for d3172c6

• Merge pull request #198 from PixelgenTechnologies/feature/exe-2061-resolve-k-value-bug

  Show description for 433e234
  johandahlberg

  authored
  433e234

  Copy full SHA for 433e234

Commits on Nov 14, 2024

• Merge pull request #199 from PixelgenTechnologies/feature/exe-2054-bail-early-on-bad-demux

  Show description for d07eace
  johandahlberg

  authored
  d07eace

  Copy full SHA for d07eace

Commits on Dec 10, 2024

• Raise error when dynamic and hard filters both on

  johandahlberg

  committed
  0a38a6f

  Copy full SHA for 0a38a6f

• Update changelog

  johandahlberg

  committed
  26cc9e7

  Copy full SHA for 26cc9e7

• Fix typo

  johandahlberg

  committed
  8a5df55

  Copy full SHA for 8a5df55

• Merge pull request #200 from PixelgenTechnologies/feature/exe-2075-fail-if-hard-and-dynamic-limit-both-set

  Show description for 542cc28
  johandahlberg

  authored
  542cc28

  Copy full SHA for 542cc28

• Set minumum threshold for the dynamic size filter

  johandahlberg

  committed
  3845df2

  Copy full SHA for 3845df2

• Better error message when all components filtered

  johandahlberg

  committed
  9899d56

  Copy full SHA for 9899d56

• Merge pull request #201 from PixelgenTechnologies/feature/exe-2065-set-hard-cutoff-for-min-size

  Show description for 45a8cdd
  johandahlberg

  authored
  45a8cdd

  Copy full SHA for 45a8cdd

• fix: changelog

  ambarrio

  committed
  577f567

  Copy full SHA for 577f567

• fix: changelog

  ambarrio

  committed
  6fe1062

  Copy full SHA for 6fe1062

• Update CHANGELOG.md

  Show description for 702c122
  

  ambarrio

  and

  johandahlberg

  authored
  702c122

  Copy full SHA for 702c122

• Merge pull request #202 from PixelgenTechnologies/release-0.19

  Show description for 243cc4c
  ambarrio

  authored
  243cc4c

  Copy full SHA for 243cc4c