0.6.1

• feat(MarkersPlot): enhance subset handling for metadata columns
• chore(MarkersPlot): default cluster_columns to FALSE for heatmap and dot plots
• feat(MarkersPlot): improve handling of subset and comparison parameters
• fix(MarkersPlot): fix when ident_2 is NULL while running FindMarkers
• fix(MarkersPlot): correct variable reference for order_by in JitterPlot function

Full Changelog: 0.6.0...0.6.1

0.6.0

• chore: update RoxygenNote to 7.3.3
• fix(featurestatplot): improve feature group handling in data frame
• feat(featurestatplot): default options to TRUE to show row and column names when plot_type is heatmap-alike
• feat: add downsample parameter to feature statistic plots
• chore(enrichmentplot): remove preset label_nudge parameter in BarPlot call
• feat(featurestatplot): add pos_only parameter to filter positive feature values
• feat(clonal_size_data): refactor data wrangling and grouping logic
• feat(CCCPlot): enhance meta_specificity documentation
• feat: add MarkersPlot function and documentation
• chore: add 'donttest' for examples for EnrichmentPlot function
• fix(FeatureStatPlot): handle NA values in dot size calculation
• BREAKING: remove VolcanoPlot re-exports, using MarkersPlot instead

Full Changelog: 0.5.5...0.6.0

0.5.5

• feat: enhance clone selector utilities
• feat: add comprehensive tests for clone selectors
• feat: support group2 as a number in clone selectors
• feat(CellStatPlot): allow passing values_by and values_fill for pies plot
• fix(clonal_size_data): fix when grouping is not Sample

Full Changelog: 0.5.4...0.5.5

0.5.4

• docs(README): update credits section with additional packages
• feat(ClonalResidency): allow multiple specific comparisons for groups
• feat: support clone selectros to be used in dplyr verbs (e.g., mutate)
• docs(README): update Clonal Plots references

Full Changelog: 0.5.3...0.5.4

0.5.3

• feat(EnrichmentPlot): add support for heatmap plot type and new values_fill parameter
• fix(EnrichmentPlot): improve error handling for enrichr data preparation

Full Changelog: 0.5.2...0.5.3

0.5.2

• fix(EnrichmentPlot): ensure unique top terms in EnrichmentPlot by disabling ties in slice_min
• fix(CellDimPlot/FeatureStatPlot): fix when reduction is only on a subset of cells

Full Changelog: 0.5.1...0.5.2

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