fix(FeatureStatPlot): plot features taken from meta.data for objects without a dimensional reduction, where cbind(object@meta.data, NULL) failed with “arguments imply differing number of rows”
fix(FeatureStatPlot): change error to warning for colorbar centering and set default center_limit
fix(FeatureStatPlot): remove redundant in_form argument in function call
fix(FeatureStatPlot): update default layer handling and documentation for plot types (scale.data for heatmp/dot, data otherwise)
Version 0.8.0
BREAKING: set default layer parameter to “scale.data” in FeatureStatPlot and update documentation
BREAKING: add group_by and flatten_markers parameters and revise select and each argument descriptions, improve metadata column mapping details, deprecate subset_by and subset_as_facet parameters
feat(FeatureStatPlot): add center_zero parameter to control colorbar centering⏎
fix: set default order_by parameter to “desc(abs(avg_log2FC))” in MarkersPlot function
fix: update order_by parameter to use absolute log2FC in MarkersPlot function
fix: add tidygraph to Suggests in DESCRIPTION and update comment in utils.R
fix: add methods import for slot and slotNames in NAMESPACE and utils.R
fix: update MarkersPlot function to replace deprecated subset_by with each, and update documentation accordingly
fix(ClonalGeneUsagePlot): fix passing rows_name not working for Heatmap
fix(FeatureStatPlot): fix group_by not working for ridge plots
fix(FeatureStatPlot): ensure FeatureGroups are factors with specified levels
fix(FeatureStatPlot): update bg_cutoff default value to NULL for consistency across functions
chore: use r-meta >=1.12 as conda dependency
chore(CCCPlot): use 0x2192 unicode for -> in plots
chore(CellStatPlot): use annotation name instead of row_names to hide rows name
chore(ClonalOverlapPlot): use annotation name instead of row_names
chore(FeatureStatPlot): avoid deprecation warning in the examples to adopt latest plotthis
docs(MarkersPlot): make visualization better for the examples
Version 0.7.6
fix(CCCPlot): clarify link_alpha usage in parameter documentation
fix(CCCPlot): ensure link_width_by defaults to magnitude in linkedheatmap
fix: adapt plot APIs/docs for plotthis 0.13
Version 0.7.5
fix(DESCRIPTION): specify exact version for drieslab/GiottoClass dependency
fix(DESCRIPTION): update GiottoClass and GiottoUtils dependency versions
fix(DESCRIPTION): update GiottoClass dependency to use the latest version without a specific commit
ci: update GiottoClass dependency to version 0.4.7
ci: update GiottoClass dependency to version R4.4.0
chore(DESCRIPTION): specify exact version for drieslab/GiottoClass dependency
ci: update GiottoClass and GiottoUtils dependencies to specific versions
ci: update GiottoClass dependency to use the latest version
docs: add documentation section with link to online resources [skip ci]
fix: enhance gene selection logic in MarkersPlot function for heatmap and dot plots
fix(CCCPlot): fix rows_split_by and columns_split_by for heatmp with method = ‘interaction’
docs: update LLM provider model and API endpoint in Visualizing_data_with_LLMs vignette
docs: update example in FeatureStatPlot documentation to include row annotation palette
fix: enhance handling of heatmap and dot plot types in FeatureStatPlot function
fix(FeatureStatPlot): hide column names for heatmap with cell_type bars
refactor(do_call): use do_call from plotthis
feat: add linkedheatmap plot type to CCCPlot function with new parameters for ligand and receptor expressions
docs(CCCPlot): enhance CCCPlot documentation: Update title, arguments, and descriptions for clarity and detail. Improve data format and method sections, and refine examples for better usability.
docs(CellDimPlot/CellVelocityPlot): enhance documentation for CellDimPlot and CellVelocityPlot functions
docs(CellStatPlot): enhance CellStatPlot documentation and argument descriptions
docs(SCPlotterChat): enhance documentation for LLM-powered chat interface, including detailed descriptions of architecture, conversation history, tool registry, and LLM provider setup
docs: update documentation for Clonal Composition, Length, Overlap, Residency, and Volume plots
docs: enhance ClonalDiversityPlot and ClonalRarefactionPlot documentation for clarity and detail
docs(ClonalGeneUsagePlot): enhance documentation for clarity and detail, including usage examples and parameter descriptions
docs: update documentation for ClonalKmerPlot and ClonalPositionalPlot
docs: enhance ClonalStatPlot documentation with detailed arguments and usage examples
docs: enhance documentation for clonal data processing functions, improving clarity and detail
docs: enhance ClustreePlot documentation for clarity and detail, including usage examples and parameter descriptions
docs: enhance EnrichmentPlot documentation for clarity and detail, including comprehensive parameter descriptions and usage examples
docs: enhance FeatureStatPlot documentation and internal dispatcher
docs: enhance MarkersPlot documentation for clarity and detail
docs: enhance documentation for spatial plot functions in Seurat and Giotto
docs: update documentation links and examples for clarity and consistency across multiple plot functions
Version 0.7.4
feat(ClonalStatPlot): enhance group selection (argument: groups) with named vector/list
feat(ClonalResidencyPlot): enhance group handling for scatter plots with named vectors/lists
feat(MarkersPlot): enhance selection functionality with custom filtering conditions
Version 0.7.3
fix(ClonalResidencyPlot): update data selection to include unique split_by parameter for upset plots
chore: update LLM provider configuration in vignette to use new model and API key
fix: update LLM provider model to use openai/gpt-5.4-nano in vignette
fix(ClonalResidencyPlot): remove unused title parameter and update function usage in documentation
fix(ClonalResidencyPlot): refactor segment data handling for improved readability
feat: implement default dimension reduction functions for Seurat objects
ci: update package dependencies in workflow for improved compatibility
feat(MarkersPlot): add options to show labels and customize significant markers in heatmap plots
fix: fix setting default dimreduction when “DefaultDimReduc<-` is available
fix(CellStatPlot): ensure rows_name is set correctly for heatmap arguments
refactor(CellStatPlot): remove rows_name parameter from function and documentation
chore(CellStatPlot): improve error messages for ‘group_by’ and ‘rows_by’ parameters in pie heatmap
refactor(FeatureStatPlot): comment out row and column name annotation arguments
Version 0.7.2
docs: update title and description to include spatial data analysis
refactor: make implementation of group level retaining consistant across all clonal functions
fix: set sample identity for Seurat objects in ClonalLengthPlot function
fix: adjust x-axis breaks in ClonalLengthPlot to nearest tens and handle missing breaks
chore(ClonalLengthPlot): add default value for position_dodge_preserve
Version 0.7.1
fix(ClonalStatPlot): streamline xlab assignment for clarity in plots
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(utils): implement do_call function for improved performance in function calls
feat(CellStatPlot): refactor Heatmap call to use do_call for improved argument handling
feat(ClonalStatPlot): refactor Heatmap call to use do_call for improved argument handling
feat(CellStatPlot): enhance’rows_by’ and ‘rows_split_by’ parameters in heatmap plots
feat(ClonalStatPlot): support subgroup_by for heatmap
ci: update ggrepel package version to 0.9.5 in dependencies (0.9.6 requires R 4.5)
fix(ClonalVolumePlot): ensure grouping_levels are simplified correctly (fixing order not working)
