SPAC v0.9.2

What's Changed

• Refactor: Replace galaxy_tools with tools folder by @fangliu117 in #419
• merge dev to release_dev with changes of tools and README by @fangliu117 in #420
• merge to main from Release dev by @fangliu117 in #421
• merge dev to release_dev with cleanup by @fangliu117 in #422
• cleanup: remove stale CSV files from tests/templates by @fangliu117 in #423
• merge Release dev to main with cleanup by @fangliu117 in #424

Full Changelog: v0.9.1...v0.9.2

SPAC v0.9.1

What's Changed

• feat(qc-metrics): add common single cell quality control metrics by @abombin in #352
• feat(qc_summary_statistics): add summary statistics table for sc/spatial transcriptomics quality control metrics by @abombin in #353
• feat(visualize_ripley_template): add visualize_ripley_template and un… by @fangliu117 in #358
• feat(template_utils): add template_utils and unit tests by @fangliu117 in #356
• Refactor/ripley l template by @fangliu117 in #357
• Refactor: template-utils with review fixes by @fangliu117 in #359
• fix(ripley_template): address review comments - replace debug prints … by @fangliu117 in #360
• feat(setup_analysis_template): add setup_analysis_template function a… by @fangliu117 in #362
• Template load csv by @fangliu117 in #361
• feat(boxplot_template): add boxplot_template function and unit tests by @fangliu117 in #363
• feat(histogram_template): add histogram_template and unit tests by @fangliu117 in #364
• feat(spatial_plot_temp): add spatial_plot_template.py and unit tests by @fangliu117 in #365
• feat(arcsinh_normalization_template): add arcsinh_normalization_templ… by @fangliu117 in #366
• feat(zscore_normalization_template): add zscore_normalization_templat… by @fangliu117 in #367
• feat(summarize_dataframe_template): add summarize_dataframe_template … by @fangliu117 in #368
• feat(combine_annotations_template): add combine_annotations_template … by @fangliu117 in #369
• feat(manual_phenotyping_template): add manual_phenotyping_template fu… by @fangliu117 in #370
• feat(hierarchical_heatmap_template): add hierarchical_heatmap_templat… by @fangliu117 in #371
• feat(utag_clustering_template): add utag_clustering_template and unit… by @fangliu117 in #372
• feat(umap_transformation_template): add umap_transformation_template … by @fangliu117 in #373
• feat(phenograph_clustering_template): add phenograph_clustering_templ… by @fangliu117 in #374
• feat(umap_tsne_pca_template): add umap_tsne_pca_template function and… by @fangliu117 in #375
• feat(rename_labels_template): add rename_labels_template function and… by @fangliu117 in #376
• feat(relational_heatmap_template): add relational_heatmap_template fu… by @fangliu117 in #377
• feat(sankey_plot_template): add sankey_plot_template function and uni… by @fangliu117 in #378
• feat(neighborhood_profile_template): add neighborhood_profile_templat… by @fangliu117 in #379
• feat(analysis_to_csv_template): add analysis_to_csv_template function… by @fangliu117 in #380
• feat(summarize_annotation_statistics): add summarize_annotation_stati… by @fangliu117 in #381
• feat(interactive_spatial_plot_template): add interactive_spatial_plot… by @fangliu117 in #382
• feat(spatial_interaction_template): add spatial_interaction_template … by @fangliu117 in #383
• feat(nearest_neighbor_calculation_template): add nearest_neighbor_cal… by @fangliu117 in #384
• feat(visualize_nearest_neighbor_template): add visualize_nearest_neig… by @fangliu117 in #385
• feat(template_utils): add string_list_to_dictionary to template utils by @fangliu117 in #386
• feat(add_pin_color_rule_template): add add_pin_color_rule_template fn… by @fangliu117 in #387
• feat(append_annotation_template): add append_annotation_template func… by @fangliu117 in #388
• feat(binary_to_categorical_annotation_template): add binary_to_catego… by @fangliu117 in #389
• feat(calculate_centroid_template): add calculate_centroid_template fu… by @fangliu117 in #390
• feat(select_values_template): add select_values_template function and… by @fangliu117 in #391
• fix(select_values_template): fix pandas/numpy version compatibility i… by @fangliu117 in #392
• feat(downsample_cells_template): add downsample_cells_template functi… by @fangliu117 in #393
• feat(combine_dataframes_template): add combine_dataframes_template fu… by @fangliu117 in #394
• feat(subset_analysis_template): add subset_analysis_template function… by @fangliu117 in #395
• feat(quantile_scaling_template): refactor nidap code, add quantile_sc… by @fangliu117 in #396
• feat(normalize_batch_template): add normalize_batch_template function… by @fangliu117 in #397
• feat(tsne_analysis_template): add tsne_analysis_template function and… by @fangliu117 in #398
• feat(posit_it_python_template): add posit_it_python_template function… by @fangliu117 in #399
• feat: Add SPAC boxplot Galaxy tool for Docker deployment by @fangliu117 in #400
• feat: add spac arcsinh_norm interactive_spatial_plot galaxy tools by @fangliu117 in #401
• feat: add spac_setup_analysis galaxy tools by @fangliu117 in #402
• feat: add spac_zscore_normalization galaxy tools by @fangliu117 in #403
• refactor: streamline galaxy tools implementation by @fangliu117 in #405
• feat: add refactored galaxy tools by @fangliu117 in #407
• Benchmark script by @Ahmad8864 in #408
• fix(nearest_neighbor_template): Break the title in two lines by @georgezakinih in #409
• refactor all templates and unit tests by @fangliu117 in #415
• fix: Remove 6 deprecated templates (sync with tools_refactor) by @fangliu117 in #416
• merge dev to release_dev for updated spac templates by @fangliu117 in #417
• merge Release dev to main by @fangliu117 in #418

Full Changelog: v0.9.0-Public...v0.9.1

SPAC v0.9.0 Public Release

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

v0.9.0

What's Changed

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

New Contributors

• @Ahmad8864 made their first contribution in #308
• @ying39purdue made their first contribution in #322

Full Changelog: v0.8.2...v0.9.0

v0.8.2

What's Changed

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

New Contributors

• @oeldaghar made their first contribution in #249
• @abombin made their first contribution in #275

Full Changelog: v0.7.0...v0.8.2

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.

v0.3.0

docs(version): Automatic Version Bumping

v0.2.0 release

Merge pull request #70 from FNLCR-DMAP/dev

Minor updates from NIDAP application