- chore: bump biopipen to 1.2.5 - make/add `envs.error` to control subsetting resulting empty Seurat object for `MarkersFinder`, `TopExpressingGenes`, `ScFGSEA` and `PseudoBulkDEG` processes - chore(scrna.SeuratClusterStats): make 3d dimplots share the same assets - chore(docker): upgrade R version to v4.4 - chore: update r-plotthis version to 0.11.1=r44_1 in environment_rpkgs.yml - chore: update r-scplotter version to 0.7.2=r44_2 in environment_rpkgs.yml - chore: update r-biopipen.utils version to 0.3.10=r44_2 in environment_rpkgs.yml - allow genes as features in cell qc plots for SeuratPreparing) - feat(utils.slugify): add strip parameter to control leading/trailing non-alphanumeric character removal (may BREAK existing runs if slugs are used for file naming) - chore: remove numpy degrading from Dockerfile (as numba supports numpy 2.4 now) - test: correct file path in assertions for sampleinfo and clustermarkers tests (because of biopipen.utils::slugify change) ## What's Changed * 2.4.4 by @pwwang in https://github.com/pwwang/immunopipe/pull/90 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.4.3...2.4.4

- chore: update pipen-cli-gbatch version to 1.1.4 - chore: update r-plotthis to 0.11.0-9 and r-scplotter version to 0.7.1-4 in environment_rpkgs.yml - fix(ClonalStatPlot): fix xlabs - feat(CellStatPlot): support plot pies as heatmap - feat(ClonalStatPlot): add subgroup_by for heatmaps - feat(ClonalResidencyPlot): add group_by_sep parameter for combining multiple group_by columns - feat(ClonalResidencyPlot): add with_class parameter to control clonal class inclusion in plots - feat: make default plot size estimation more precise - chore: update biopipen version to 1.2.2 - fix(scrna.SeuratClusterStats): fix missing cluster names in pies plot when group_by is used - feat(scrna.ModuleScoreCalculator): add support for mouse cell cycle genes in module scoring - chore(scrna.MarkersFinder): add devpars for Dot Plot dimensions - feat(scrna.SeuratClusterStats): add 'add_box' parameter to ngenes_defaults for enhanced plotting options - chore: update r-biopipen.utils to 0.3.8-4 - fix(LoadSeuratAndPerformQC): fix cell_meta object not found for loom or h5 input - feat: support specifying relative `devpars$width` and `devpars$height` for plots - fix(RunSeuratUMAP): set default metric to correlation for UMAP when using umap-learn - fix(RunSeuratDEAnalysis): fix handling subsetted object - chore: bump pipen to 1.1.11 - feat: support templated configuration file for the pipeline ## What's Changed * 2.4.3 by @pwwang in https://github.com/pwwang/immunopipe/pull/89 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.4.2...2.4.3

- chore: update r-biopipen.utils to 0.3.7=r43_3, r-scplotter to 0.7.0=r43_2, and r-plotthis to 0.11.0=r43_1 in environment_rpkgs.yml - BREAKING(clone_selectors): change 'groups' to 'group_by' - BREAKING(ClonalStatPlot): change behavior of clone selecting (now it is only controlled by `clones` argument) - feat(ClonalStatPlot): add support for chord and circos plot types in ClonalStatPlot function - feat: remove deprecated ClonalDynamicsPlot function - chore: update biopipen version to 1.1.14 in pyproject.toml - fix(scrna.SeuratClustersStats): fix empty identity in description of default dimplots - feat(scrna.SeuratClusterStats): support 3D dimplots ## What's Changed * 2.4.2 by @pwwang in https://github.com/pwwang/immunopipe/pull/88 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.4.1...2.4.2

- chore: update SeuratPreparing and ClusterMarkers configurations - chore: update ClusterMarkers to select top 5 markers for each cluster - fix: make sure SeuratClustering is included in the pipeline along with CellTypeAnnotation - chore: update biopipen to 1.1.12 - fix(tcr.ScRepLoading): remove records with IG? or TR? chains to prevent errors in combineTCR and combineBCR - chore(scrna.SeuratClusterStats): set default options for pies plot for stats - fix(scrna.SeuratClusterStats): improve plot description handling when plot_type is not given - chore: update r-plotthis version to 0.10.1=r43_10 in environment_rpkgs.yml - fix: update BarPlotSingle to conditionally use geom_text for flipped plots and adjust height/width calculations - fix(Box/ViolinPlo): hide legends for color, size, and alpha scales for highlighted points - fix(BeeswarmPlot):fix highlight not working - fix(JitterPlot): fix `position_jitterdodge()` requires at least one aesthetic to dodge by for ggplot2 v3 - fix(BarPlot): correct conditional assignment for `fill_by` parameter - fix(BarPlot): fix when x has multiple columns - feat(Heatmap): add rows_orderby and columns_orderby to order rows and columns (if set, cluster_rows and cluster_columns will default to FALSE) - fix(Heatmap): ensure ordered factors are converted to character for proper processing - BREAKING(Box/ViolinPlot): update sort_x parameter to accept expressions for x-axis ordering - fix(TrendPlot): complete missing combinations for area layer to prevent interpolation issues - fix(AreaPlot): complete missing combinations for x, group_by, and facet_by to prevent interpolation issues - feat(RadarPlot): add groups parameter to filter and order groups in the plot - fix(RadarPlot): clarify groups parameter documentation and its implications on keep_empty - fix: ensure unique values in for loops for grouping in bar, pie, ring, and trend plots - chore: update r-scplotter version to 0.6.6=r43_10 in environment_rpkgs.ym - fix: update fill parameter in BarPlot function for enrichment plots (adopting plotthis v0.10.1) - chore: improve error message for missing 'group_by' in ClonalCompositionPlot for box/violin plots - fix: enhance clonal size data function to handle empty groupings and improve data processing - docs: update ClonalVolumePlot examples to include fill_by parameter to adopt plotthis v0.10.1 - feat: expand ClonalStatPlot functionality with new plot types (col-rel and col-abs) - fix: update data binding in CellDimPlot to exclude redundant metadata columns - feat: add agg parameter to CellStatPlot for custom summarization - feat: rename `return_ids` to `ouput` for clone selectors so that they can return logicals (booleans) for selection - feat: clone selectors gain a `output_within` option to return the selection results within a specific subset - feat(ClonalResidencyPlot): make the plot symmetric when numbers of clones are imbalanced between the two groups and allow specifying the palette for the plot - chore: update r-biopipen.utils version to 0.3.6=r43_10 in environment_rpkgs.yml - fix(RunSeuratSubClustering): prioritize integrated_new_reduction in UMAP reduction assignment - fix(RunSeurat*): replace dot notation with bracket notation for reduction assignment - feat(LoadSeuratAndPerformQC): support ParseBio data - feat(RunSeuratCellCycleScoring): add function to perform cell cycle scoring in Seurat objects - feat: update LoadSeuratAndPerformQC and RunSeuratCellCycleScoring to support cell cycle scoring arguments - feat(RunSeuratCellCycleScoring): optimize memory usage by cleaning up unnecessary assays - feat(RunSeurat): enhance logging and expand dimensions handling in PCA and UMAP functions - chore(VizDEGs): set select to 5 for heatmap_* plots ## What's Changed * 2.4.0 by @pwwang in https://github.com/pwwang/immunopipe/pull/86 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.3.3...2.4.0

- docs: clarify caching mechanism configuration in the pipeline - feat: add logging of Immunopipe version information in gbatch command - chore: bump pipen-cli-gbatch to v1.1.2 - chore: update biopipen dependency version to ^1.1.11 - feat(scrna_metabolic_landscape): support multiple subset_by columns in Seurat object expansion - fix(scrna.SeuratClusterStats): fix dimplots for clusters from subclustering - fix(scrna.SeuratSubClustering): correct argument references in RunSeuratSubClustering function - fix(scrna.SeuratClusterStats): handle reduction assignment for subclustering based on plot type and identity - fix(scrna.SeuratClusterStats): ensure either 'group_by' or 'ident' is specified in dimplots, not both - feat(tcr.ScRepLoading): improve handling of contig file formats for 10X data - feat(scrna.SeuratPreparing): add cell cycle scoring functionality to Seurat object preparation - fix(scrna.MarkersFinder): improve plot argument handling for subset by group and plot types - feat(tcr.ScRepLoading): support loading from prefixed contig files - fix(scrna.CellTypeAnnotation): fix sctype not working ## What's Changed * 2.3.3 by @pwwang in https://github.com/pwwang/immunopipe/pull/84 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.3.2...2.3.3

- chore: chore: update Dockerfile to install numpy version 2.3 for compatibility with scanpy - chore: add pwwang::r-sccatch to environment_base.yml - chore: update r-plotthis dependency version to 0.9.4 - chore: update r-scplotter dependency version to 0.6.5 - feat: clone selectors gain a `within` option to select clones within a specific subset - feat: clone selectors `and`/`or` support multiple selectors (more than 2) - chore: update biopipen dependency version to 1.1.5 - fix(scrna.MarkersFinder): update database handling in enrichment plots in case it is from gmt files - fix(scrna.PseudoBulkDEG): update database handling in enrichment plots to use unique databases in case gmt files were used - fix(scrna.CellTypeAnnotation): ensure at least 2 clusters for cell type annotation for scCATCH - feat(tcr.ClonalStats): add caching functionality for plots - feat(scrna.ScFGSEA): add caching functionality for GSEA results - feat(scrna.CellTypeAnnotation): enhance cell type annotation functionality to support dict input for direct annotations ## What's Changed * 2.3.1 by @pwwang in https://github.com/pwwang/immunopipe/pull/81 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.3.0...2.3.1

- chore: bump pipen to v1.1 so asynchronous path operations are supported - refactor: convert synchronous methods to asynchronous in gbatch.py - feat: add example configuration file - fix: update header reading method in validate_config to use read_text - docs: update process documentation with additional references and image links - docs: update installation and running documentation to reflect dependency changes - docs: add FAQ entry for mouse data support in the pipeline - chore: update r-biopipen.utils version to 0.3.5 in environment_rpkgs.yml - fix(RunSeuratDEAnalysis): handle +Inf/-Inf values in avg_log2FC to make visualization works - chore: bump biopipen to 1.1.1 - docs(tcr.ClonalStats): correct typo in documentation for ClonalStatsPlot reference ## What's Changed * 2.3.0 by @pwwang in https://github.com/pwwang/immunopipe/pull/80 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.2.2...2.3.0

- docs: update docs for ClusterMarkers with examples - ci: update biopipen dependency for tests - feat: add new tests and configuration for ScRepLoading, ScRepCombiningExpression and SeuratClusterStats - test: add test for clustermarkers - test: add test for TOrBCellSelection - docs: enhance documentation for PseudoBulkDEG and MarkersFinder - test: add ClonalStats tests and configuration - test: add ScFGSEA tests and configuration - test: add CellCellCommunication and CellCellCommunicationPlots tests - docs: update ScrnaMetabolicLandscape doc images - chore: bump biopipen to 0.34.17 - fix(scrna.MarkersFinder): enhance error handling in enrichment plotting and fix all-enrich plots when ident_1 is NULL - fix(tcr.ClonalStats): replace deprecated ClonalDynamicsPlot with ClonalStatPlot ## What's Changed * 2.1.3 by @pwwang in https://github.com/pwwang/immunopipe/pull/76 **Full Changelog**: https://github.com/pwwang/immunopipe/compare/2.1.2...2.1.3