0.7.0

• fix(clone_selectors): make selectors work for data from clonal_size_data()
• feat(clone_selectors): add top and order arguments to sel() and top() functions for improved selection control
• 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
• feat(CellDimPlot): add examples for setting seed and 3D plotting

Full Changelog: 0.6.6...0.7.0

0.6.6

• feat: add argument ident as alias of group_by to CellDimPlot and CellVelocityPlot
• fix: update condition for group_by and ident validation in CellDimPlot and CellVelocityPlot functions
• 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
• fix: ensure groups are treated as factors in long format and update group_by behavior
• BREAKING(clone-selectors): replace return_ids with output to allow return logicals
• feat(clone-selectors): enhance clone selection functions to support output_within parameter
• fix(ClonalScatterPlot): normalize counts using maximum of sum counts to avoid skewed plot with imbalanced number of clones for the two groups
• feat(ClonalScatterPlot): allow changing the color palette and set the default palette to turbo

Full Changelog: 0.6.5...0.6.6

0.6.5

• docs(clonalutils): add glimpse for long data in examples
• feat(clonalutils): add 'within' parameter to selection select clones within a subset
• feat(clonalutils): enhance logical operations by adding support for additional vectors in 'and' and 'or' functions
• fix: keep orders (levels of factors) of grouping variables for clonal functions

Full Changelog: 0.6.4...0.6.5

0.6.4

• feat: add subset_seurat function for automatic layer repair in Seurat v5 objects
• fix(MarkersPlot): exclude groups that failed DE analysis from plotting
• fix(SCPlotterChat): suppress plot display by redirecting to a null device
• feat(SCPlotterChat): display the code run by LLM to generate the plot
• fix(SCPlotterChat): optimize the prompts for better and more accurate output
• ci: comment out cran URL in main.yml
• ci: update extra-packages to include gsl@2.1-8 for compatibility with R>4.5
• fix(SCPlotterChat): correct ellipsis (non-ASCII) formatting in decision process comments to ASCII characters

Full Changelog: 0.6.3...0.6.4

0.6.3

• docs(vignette): update LLM model from gpt-4o-mini to gpt-5-nano for improved performance
• chore(DESCRIPTION): pin scRepertoire version to 2.2.1 for compatibility
• chore: update R version to 4.5.0 and adjust scRepertoire dependency for compatibility
• chore update GiottoClass remote reference to the latest version
• ci: update R version from 4.4.1 to 4.4.3 for compatibility
• ci: restore R dependencies setup in workflow for improved package management
• fix(conda) pin bioconductor-screpertoire version
• fix(ClonalDiversityPlot): fix calculating Gini coefficient
• fix(MarkersPlot): handle errors when subsetting object features

Full Changelog: 0.6.2...0.6.3

0.6.2

• feat(CloneSelectors): default order to "-.n" for top() for long format data
• feat: add AI coding agent instructions for scplotter
• test: fix tests for top() when default order to "-.n"
• fix(MarkersPlot): swap subsetting genes and comparisons to avoid "incorrect number of dimensions" error
• fix(screp_subset): update Seurat object handling to use tidyseurat
• fix(ClonalLengthPlot): ensure quantile breaks are unname'd (actual number instead of percentile)
• fix(ClonalLengthPlot): adjust quantile breaks calculation for bar plot
• chore(screp_subset): ensure 'tidyseurat' package is required for filtering Seurat objects
• fix(clonal_size_data): update names_sep to names_pattern for better regex handling
• fix(MarkersPlot): set default value_fill to 0 for improved heatmap visualization
• docs(vignette): update LLM model from gpt-4o-mini to gpt-5-nano for improved performance
• chore(DESCRIPTION): pin scRepertoire version to 2.2.1 for compatibility
• ci: update R version from 4.4.1 to 4.4.3 for compatibility

Full Changelog: 0.6.1...0.6.2

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