SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - SPAC v0.9.0 Public Release

This release is the public release with efforts to provide better documentations.

- Jupyter Notebook
Published by ruiheesi 6 months ago

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - v0.9.0

What's Changed

• perf: updating the default colormap for interactive spatial to rainbow by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/300
• feat: adding automated bin cal to histogram by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/301
• Histo title log by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/304
• log(manual_phenotype): Added a statement clarifying that cells could … by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/302
• Interactive spatial color map by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/305
• refactor(interactivespatialplot): added a verbose title by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/306
• interactive spatial plot with features by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/307
• Boxplot Plotly Implementation by @Ahmad8864 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/308
• Summarize dataframe by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/310
• fix(interactivespatialplot): fixed typos in api name and arguments by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/309
• releasing summarize dataset and fixed interactive spatial plot by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/311
• fix(presentsummaryas_figure): fixed json conversion when non python… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/314
• Ripley l by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/313
• Ripley L with edge correction, and summarize data frame handling non native python types by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/315
• feat(ripley_l): Added edge correction parameter to the high level fun… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/316
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/317
• Add Static Plotly Figure Return Type by @Ahmad8864 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/312
• Histogram Precomputation by @Ahmad8864 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/319
• fix(relational_heatmap): adjusted the flipped axis labels by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/320
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/321
• Fix Histogram Return Value by @Ahmad8864 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/324
• refactor histogram by returning hist_data by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/325
• Spatial annos by @ying39purdue in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/322
• Add paper directory and files by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/327
• KNN Clustering by @oeldaghar in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/271
• fix(select_values): added support when observation are numerical by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/331
• Add comments UTAG tests by @abombin in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/332
• fix(summarize_dataframe): remove duplicated missing index by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/338
• feat(visualizenearestneighbor): add pin-color and corresponding uni… by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/339
• merge updated summarizedataframe and visualizenearestneighbor with pin-color from dev to releasedev by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/340
• feat(pin_color): add pin color feature to visualize nearest neighbor … by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/341
• merge dev into releasedev with updated visualizenearest_neighbor by adding pin-color feature by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/342
• fix(visualizenearestneighbor): rewrite unit tests and move up libr… by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/343
• merge the updated visualizenearestneighbor function and unit tests from dev to dev_release by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/345
• step: bumping minor version from 0.8 to 0.9 by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/346
• step: bumping minor version from 0.8 to 0.9 by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/347
• Minor version bumping from v0.8.0 to v0.9.0 by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/348

New Contributors

• @Ahmad8864 made their first contribution in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/308
• @ying39purdue made their first contribution in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/322

Full Changelog: https://github.com/FNLCR-DMAP/SCSAWorkflow/compare/v0.8.2...v0.9.0

- Jupyter Notebook
Published by ruiheesi about 1 year ago

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - v0.8.2

What's Changed

• fix(batch_normalize): add annotation and layer checks by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/225
• add annotation and layer check for batch_normalize by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/226
• perf: deming CD by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/227
• feat(assignmanualphenotypes): Function to define and associate manu… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/228
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/229
• test(assignmanualphenotypes): added tests for prefix and suffix sup… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/230
• fix(calculate_centroid): add new columns in a single operation by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/231
• fix(calculate_centroid): add new columns in a single operation by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/232
• Ripley l by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/172
• fix(histogram): return a single Axes and fix corner case of normalize… by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/233
• fix the histogram and normalizefeaturescore functions by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/234
• Ripley l by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/236
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/237
• Test ripley precision by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/235
• fix(ripleyl): Generate write warning messages for nobservations and… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/238
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/239
• Ripley l by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/240
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/241
• perf(plotripleyl): Printed the warning when phenotype is missing in… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/243
• feat(combine_annotations): Data utility to combine multiple annotaito… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/242
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/244
• fix(ripley_l): Convert annotation to categorical before calling core … by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/246
• test(combine_annotation): Added test to check that the annotation lis… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/245
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/247
• feat: Adding pin color function and tests by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/190
• update to documentation by @oeldaghar in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/249
• Added feature subsetting unit tests for raw data by @oeldaghar in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/248
• feat(select_values): Added option to exclude values by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/251
• test(select_values): Added test to the case where both include and ex… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/252
• refactor(selectvalues): split selectvalues into core functions for … by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/253
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/254
• doc(select_values): Updated documentation by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/255
• Manual phenotyping by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/256
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/257
• perf(assignmanualphenotypes): Replace apply method with vectorized … by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/258
• Manual phenotype to use dot instead of apply by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/259
• feat(plotripleyl): Return a dataframe of the line plots by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/260
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/261
• fix: double log in boxplot and add log in histogram and update unit t… by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/264
• merge updated boxplot and histogram with log modification from dev to release_dev by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/265
• fix(boxplot): replace the calculation of expected_values with hard-co… by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/268
• feat(checklabel): add a new utils function checklabel and correspon… by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/269
• feat: add calculate spatial distance feature and coresponding unit tests by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/263
• T2 spatial interaction by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/270
• fix: store the output in adata.obsm and remove subset by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/274
• fix: replace name spatialdistance with nearestneighbor by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/276
• fix: remove testcalculatespatial_distance in remote repo by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/277
• T2 2024 update: include dataframe return by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/278
• T2 interactive spatial plot by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/273
• feat: create visualize nearest neighbor related functions and tests by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/280
• T2 update first dev deployment by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/283
• perf: add verbose for default get label method by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/284
• minor update for interactive spatial plot by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/285
• refactor(plotripleyl): Added appropriate error messages and fixed t… by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/286
• step: version 0.8.0 release by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/288
• SPAC version 0.8.0 release by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/289
• SPAC version 0.8.0 release by @ruiheesi in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/290
• Bug fixes and refactoring for Shiny app by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/291
• refactor(hierarchical_heatmap): Removed hard coded cmap by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/292
• Add utag clustering by @abombin in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/275
• test(resol): lower resolution for UTAG clustering by @abombin in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/294
• Dev by @georgezakinih in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/295
• fix(calculatenearestneighbor): reindex to match adata.obs and unit test by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/296
• fix(select_values): adata.obsm remain numpy arrays by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/297
• merge selectvalues and calculatenearestneighbor to releasedev by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/298
• merge releasedev to main for the updates of selectvalues and calculate_NN by @fangliu117 in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/299

New Contributors

• @oeldaghar made their first contribution in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/249
• @abombin made their first contribution in https://github.com/FNLCR-DMAP/SCSAWorkflow/pull/275

Full Changelog: https://github.com/FNLCR-DMAP/SCSAWorkflow/compare/v0.7.0...v0.8.2

- Jupyter Notebook
Published by ruiheesi over 1 year ago

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - v0.7.0

This production release is available on NIDAP as well. The dependency requires python for 3.8, we are actively moving towards higher python version.

- Jupyter Notebook
Published by ruiheesi almost 2 years ago

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - v0.3.0

- Jupyter Notebook
Published by ruiheesi over 2 years ago

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplexed Imaging - v0.2.0 release

- Jupyter Notebook
Published by ruiheesi almost 3 years ago