0.5.1

• feat: enhance EnrichmentPlot function to support enrichR data format
• chore: adopt updated Heatmap function from plotthis v0.7.2
• docs: update ClonalCompositionPlot examples to include clone_split parameter

Full Changelog: 0.5.0...0.5.1

0.5.0

New features:

• feat: support giotto objects for CellDimPlot, CellStatPlot and FeatureStatPlot
• feat: add CellVelocityPlot function for visualizing cell velocities in Seurat and Giotto objects (#11)
• feat: add .h5ad file support for scRNA-seq data visualization
• docs: update spatial example notebooks to use cutoff for feature plots (introduced by plotthis v0.7.2)

Fixes

• fix: adjust x and y coordinates for Nanostring CosMx data prepared by Seurat

House keeping

• enh: slim ifnb_sub and pancreas_sub datasets to reduce the size of the package

Full Changelog: 0.4.0...0.5.0

0.4.0

• docs: add example for Box/Violin plot for CellStatPlot
• chore(CellStatPlot): default 'ident' of to the active.ident of given object
• chore: remove references to PrepareEnrichrResult from NAMESPACE, reexports, and documentation (plotthis v0.7)
• docs: fix links for venn and upset plot references in ClonalResidencyPlot documentation
• chore: rename clonalstatplot.R to clonalcompositionplot.R
• refactor: rename 'select' to 'sel' in clone selection functions and documentation
• feat: deprecate ClonalDynamicsPLot in favor of ClonalStatPlot
• BREAKING: change clone selectors: larger to gt and ge; smaller to lt and le; add ne
• feat: add ClonalStatPlot function for visualizing clone statistics
• fix: fix empty groupings for merge_clonal_groupings
• docs: correct VignetteIndexEntry title in Visualizing_data_with_LLMs
• feat: add plots spatial data (wip)
• chore: add terra package to DESCRIPTION
• feat(spatial): add Spatial.Seurat.SlideSeq
• enh(FeatureStatPlot): allow ident to be NULL so that Idents() is used
• feat(SpatPlot): add spatial plots for Xenium data by Giotto
• chore: fix checks
• ci: add GiottoClass to extra-packages for R dependencies
• ci: use R 4.4.1 (required by GiottoClass)
• doc: finish vignettes for xenium data with giotto
• feat: add spatial utilities for plotting in Seurat and Giotto
• doc(spatial): finish documentation for spatial plots
• doc: add CODEX examples for spatial plots
• doc: add vignettes for scplotter with Giotto seqFISH and vizgen data
• chore: bump version to 0.4.0
• doc: enhance documentation for SpatFeaturePlot and SpatDimPlot with additional resource links for examples

Full Changelog: 0.3.0...0.4.0

0.3.0

• enh(CCCPlot): allow specifying aggregation method for magnitude score
• chore(CCCPlot): default magnitude_agg to length (number of interactions)
• enh(CCCPlot): add support for box, violin, and ridge plot types
• fix(ClonalOverlapPlot): adopt plotthis 0.6.2 for label in heatmap
• docs(FeatureStatPlot): make comparisons work in example
• docs: add donttest to examples in multiple plot functions and documentation
• enh(CelDimPlot): set default group_by to "Identity" if not provided
• feat: add SCPlotterChat class for chat functionality
• docs: add donttest to examples in ClonalVolumePlot, ClonalAbundancePlot, and ClonalResidencyPlot functions
• chore: update scRepertoire dependency (BorchLab/scRepertoire#493)

Full Changelog: 0.2.2...0.3.0

0.2.2

• fix: fix 'split_by' not working for various plot types in CCCPlot

Full Changelog: 0.2.1...0.2.2

0.2.1

• docs: update examples in documentation to use vector format for genes in ClonalGeneUsagePlot
• fix: handle 'split_by' parameter in ChordPlot for two genes in ClonalGeneUsagePlot
• docs: update image syntax in README to remove unwanted captions
• fix: include 'group_by' in grouping for bar plot in FeatureStatPlot

Full Changelog: 0.2.0...0.2.1

0.2.0

• feat: enhance CellStatPlot to support violin and box plots
• fix(ClonalDiversity): fix n_boots not working
• feat(ClonalDiversityPlot): add methods d50 and dXX
• fix: fix 'scale = TRUE' not working for ClonalCompositionPlot with method "homeo"
• refactor: move clonal util functions to a separate file
• feat: add ClonalDynamicsPlot and update documentation
• fix: fix all places using SankeyPlot to adopt plotthis 0.5.1
• docs: fix cross-links to plotthis functions
• fix: update DESCRIPTION to include additional remote repository
• fix: update documentation to use scplotter functions in examples

Full Changelog: 0.1.2...0.2.0

0.1.2

• feat: allow scale of ClonalCompositionPlot to be TRUE/"sample"/FALSE

Full Changelog: 0.1.1...0.1.2

0.1.1

• deps: add pwwang::bioconductor-screpertoire to conda requirements
• fix: fix Some of the methods for ClonalDiversityPlot not working (#5)
• docs: fix link for scRepertoire in README
• docs: update README to expand full name of CCCPlot
• deps: add gglogger as a suggest dependency
• feat: allow to use facet_by when plot_type = 'dim' for FeatureStatPlot
• deps: remove Remotes in DESCRIPTION (plotthis is on CRAN now)
• docs: fix URLs in README and other docs

Full Changelog: 0.1.0...0.1.1

0.1.0

• feat: add ClonalVolumePlot, ClonalAbundancePlot, ClonalLengthPlot, ClonalResidencyPlot and ClonalCompositionPlot
• style: fix R CMD check
• deps: update Remotes in DESCRIPTION file to use latest scRepertoire
• style: update .Rbuildignore and .github/workflows/main.yml to fix CMD check issues
• style: fix CMD check issues
• style: fix CMD check issues
• style: fix CMD check issues
• style: fix CMD check issues
• feat: add ClonalOverlapPlot
• feat: add ClonalDiversityPlot
• feat: add ClonalGeneUsagePlot, ClonalPositionalPlot and ClonalPositionalPlot
• feat: add ClonalRarefactionPlot
• feat: add CCCPlot
• feat: add radar/spider plot for CellStatPlot
• docs: update method for ClonalDiversityPlot to include gini.coeff
• docs: add CCCPlot and ClonalX plots to README and mention scRepertoire in the Credits in README

Full Changelog: 0.0.2...0.1.0