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Version 0.13.1

• BREAKING(LinkedHeatmap): update parameter names for link width and color in LinkedHeatmap and LinkedHeatmapAtomic
• BREAKING(LinkedHeatmap): replace title_gp with title_params for improved title customization
• feat(heatmap): consolidate annotation arguments into structured list params
• feat(LinkedHeatmap): enhance link width customization with constant value option
• feat: add y_brackets parameter for significance brackets in box/violin/beeswarm plots
• feat(RidgePlot): add x_min and x_max parameters for x-axis limits
• fix(heatmap): fix name annotation error when it has empty levels
• fix(heatmap): update row and column title checks to use annotation parameters
• fix(LinkedHeatmap): fix alignment when columnt_title provided for either heatmap
• fix(ViolinPlot): conditionally load ggpubr for pairwise comparisons (kassambara/ggpubr#751)
• docs: update plot descriptions for clarity and consistency across documentation

Version 0.13.0

• feat: add split_by parameter to combine_plots for enhanced data composition, especially for split plots
• feat: add LinkedHeatmap and supporting functions with documentation and tests
• feat: uniform plotting data access from plot objects
• feat: use a fast do.call across all plotting functions
• feat(dotplot): add border customization options for dots and lollipop bars (#32)
• feat(dotplot): update fill_cutoff parameter to accept string operators and improve documentation (#31)
• feat(combine_plots): enhance split_by functionality to ensure combined data is accessible and correctly structured
• feat: add prepare_continuous_color_scale() utility and refactor DimPlot
• feat: add color scale quantile/cutoff params to DotPlot, ScatterPlot, BarPlot, SplitBarPlot (#30)
• fix(chordplot): correct handling of split_by parameter when combining plots
• fix(heatmap): remove return_grob parameter and wrap heatmap with patchwork
• fix(radarplot): correct assignment of split_by variable and update combine_plots call
• fix(combine_plots): refine data handling in combine_plots function for layer-specific data integrity
• fix(utils): adjust color scale handling for edge cases in prepare_continuous_color_scale
• fix: include split_by in keep_na and keep_empty checks for FeatureDimPlot function
• style: use air to format all source files
• chore: add .codegraph to .gitignore to exclude codegraph files from version control
• chore: remove unused imports and clean up parameter documentation across multiple files
• docs: enhance documentation for color palette usage and plotting data access
• docs(Heatmap): refactor HeatmapAtomic documentation for clarity and consistency
• docs: enhance documentation for AreaPlot and AreaPlotAtomic functions
• docs: enhance documentation for SplitBarPlotAtomic and BarPlot functions
• docs: update documentation for BoxPlot, ViolinPlot, and BeeswarmPlot functions
• docs: enhance documentation for ChordPlot and ChordPlotAtomic functions
• docs: enhance RidgePlot and RidgePlotAtomic documentation and functionality
• docs: enhance documentation for DimPlot and FeatureDimPlot functions
• docs: enhance documentation for DotPlot and LollipopPlot functions
• docs: enhance documentation for ClustreePlot and ClustreePlotAtomic functions
• docs: enhance documentation for CorPairsPlotAtomic and CorPlot
• docs: update documentation for DimPlot and DimPlotAtomic parameters
• docs: update documentation for EnrichMap and EnrichNetwork functions
• docs: enhance documentation for GSEASummaryPlot and GSEAPlot functions
• docs: remove unused import for ggridges in densityplot and NAMESPACE
• docs: enhance documentation for JitterPlot and JitterPlotAtomic
• docs: update documentation for LinePlotAtomic, LinePlotGrouped, and LinePlotSingle
• docs: enhance ManhattanPlot and ManhattanPlotAtomic documentation
• docs: enhance NetworkAtomic documentation with detailed argument descriptions and architecture overview
• docs: update documentation for PieChart and PieChartAtomic functions with detailed descriptions and parameter explanations
• docs: update QQPlot and QQPlotAtomic documentation to include PP plot details and enhance parameter descriptions
• docs: enhance documentation for RadarPlotAtomic and radarplot functions
• docs: enhance documentation for RingPlot and RingPlotAtomic functions with detailed descriptions and parameter explanations
• docs: enhance documentation for RarefactionPlot and RarefactionPlotAtomic functions with detailed descriptions and parameter explanations
• docs: enhance documentation for ROCCurveAtomic and get_cutoffs_data
• docs: enhance documentation for SankeyPlot and SankeyPlotAtomic
• docs: enhance ScatterPlot and ScatterPlotAtomic documentation
• docs: improve documentation for .compute_velocity_on_grid and .flip_y functions with detailed descriptions and parameter explanations
• docs: enhance spatial visualization functions in terra package
• docs: enhance documentation for TrendPlot and TrendPlotAtomic functions with detailed descriptions and parameter explanations
• docs: update documentation for UpsetPlot and related functions
• docs: update VennDiagram and related functions for improved documentation and clarity
• docs: enhance documentation for VelocityPlot function with detailed parameter descriptions and usage examples
• docs: enhance VolcanoPlot and VolcanoPlotAtomic documentation
• docs: enhance documentation for WordCloudPlot and WordCloudPlotAtomic functions with detailed descriptions and usage examples

Version 0.12.1

• feat: enhance check_palcolor function to handle character palcolor input more robustly
• feat: add position_dodge_preserve parameter to BoxViolinPlot and BoxViolinPlotAtomic for enhanced dodging control
• feat: add CLAUDE.md for project guidance and development workflow documentation
• feat(Heatmap): add block and label annotation types with unified building, per-annotation side control, reordering, validation, and split_by support
• feat(dotplot): add size_min and size_max parameters for dot size control (#29)
• fix(.Rbuildignore): add CLAUDE.md and PDF files to ignore list
• refactor(Heatmap): move utils to a separate file
• refactor: update dplyr and tidyr functions to use all_of for column selection
• docs: add examples for CorPlot and DensityPlot functions
• test(DotPlot): suppress warnings when using fill_by for size calculation
• test(ManhattanPlot): update highlight threshold from 1e-5 to 1e-3

Version 0.12.0

• chore: update .Rbuildignore and .gitignore to exclude .vscode directory
• refactor(Heatmap): remove deprecated annotation parameters and introduce alias support
• feat(Heatmap): add default dimensions for simple annotations in Heatmap function
• fix(Heatmap): resolve annotation name and legend overlap issue in ComplexHeatmap
• feat: set default figure dimensions in pkgdown and basic design vignette
• test: add unit tests for plot functions
• ci: add missing ‘remotes’ package to workflow dependencies
• fix(Heatmap): add validation to ensure data is not empty in process_heatmap_data function
• feat(Heatmap): add draw_opts parameter for additional drawing options
• feat(Heatmap): add aspect.ratio parameter for cell dimension control
• fix(Heatmap): update cell dimension calculations to use actual matrix dimensions
• fix(Heatmap): improve handling of annotation names to prevent overlap with legends
• feat(Heatmap): add alignment options for heatmap and annotation legends
• feat(Heatmap): add label customization options including color, size, and legend title
• feat(Heatmap): add support for marks on heatmap cells with customization options
• feat(Heatmap): add base_size parameter for scaling heatmap size
• feat(Heatmap): enhance more aliases support for row and column annotations
• feat(Heatmap): improve aspect ratio handling and dimension constraints for heatmap plots
• feat(Heatmap): add support for combined label and mark cell type
• feat(Heatmap): add octagon mark type support for heatmap cells

Version 0.11.1

• feat(BoxPlot): add support for bar plots with error bars
• chore: add additional repositories link to DESCRIPTION file for ggmanh

Version 0.11.0

• feat(palette): add tableau color palettes to palette list
• feat(dimplot): add support for 3D plots using plotly for 3-component dimplots
• feat(UpsetPlot): preserve group order in compmatrix (lower table)
• feat(UpsetPlot): add combmatrix_gap parameter for row spacing in combination matrix
• feat: implement calculate_plot_dimensions() across all plot functions
• feat: enhance heatmap dimension calculations for row and column labels based on visibility settings
• feat: add padding parameter to Heatmap for customizable heatmap spacing
• fix(UpsetPlot): nudge label position in geom_text_repel for better visibility
• fix(UpsetPlot): fix ytrans not working
• fix(Heatmap): handle empty string cases for row and column name parameters in process_heatmap_data
• fix(DimPlot): hide legend for fill and color scales for marks in dimension plot
• fix(DimPlot): ensure all levels are included in the legend by keeping empty levels for stat plots
• fix(DimPlot): disable legend for line width scale in dimension plot when graph is given
• fix(Box/Violin/BeeswarmPlot): update variance check to allow more unique values for comparison
• chore(VennDiagram): change default palette to ‘Blues’
• chore(UpsetPlot): change default palette to ‘Blues’
• chore(UpsetPlot): change segment colour of labels to NA (hiding segment lines)
• ci: update ggrepel package version to 0.9.5 in dependencies (0.9.6 requires R 4.5)

Version 0.10.1

• BREAKING(Box/ViolinPlot): update sort_x parameter to accept expressions for x-axis ordering
• feat(RadarPlot): add groups parameter to filter and order groups in the plot
• 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: 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
• fix(Heatmap): ensure ordered factors are converted to character for proper processing
• 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
• 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
• fix(heatmap): ensure unique values in processed data for heatmap

Version 0.10.0

New Features

• Add keep_na and keep_empty parameters to control handling of NA and empty values across multiple plot functions: AreaPlot, BarPlot, BoxPlot, ChordPlot, DensityHistoPlot, DimPlot, DotPlot, Heatmap, JitterPlot, LinePlot, PieChart, RadarPlot, SpiderPlot, RingPlot, SankeyPlot, TrendPlot, and VelocityPlot
• Add continuous color mapping support for BarPlot and SplitBarPlot (#28)
• Allow palcolor parameter to allow replacing colors by palette

Bug Fixes

• fix: update color handling in various plot functions to ensure consistent NA value representation
• fix: enhance palette_this function to support custom colors and NA handling
• fix: add na.value parameter to scale functions for consistent NA color handling across LinePlot and BarPlotSingle
• fix: update check_keep_na and check_keep_empty functions to return named lists
• fix: update fill_by condition in BarPlotAtomic to handle missing values correctly
• fix: update breaks and limits parameters in scale_fill_manual for BarPlotSingle

Documentation

• docs: enhance documentation for keep_na and keep_empty parameters across all affected functions
• docs: enhance documentation for color palette customization and NA handling in plots

Version 0.9.3

New Features

• Add beeswarm plot support to BoxPlot and ViolinPlot (#26)

Bug Fixes

• fix(RidgePlot): drop unused levels from split_by variable
• fix(DimPlot): handle NA values in ordering for high-top and low-top options
• fix(docs): update link to all available color palettes in basic design vignette
• fix(docs): update link format for all available palettes in palette_this documentation
• fix(docs): remove outdated link to all available palettes in documentation

Documentation

• docs: add BeeswarmPlot to the list of available plots in README

Full Changelog: 0.9.1…0.9.3

Note: Version 0.9.2 was skipped due to CRAN submission failure.

Version 0.9.1

New Features

• feat: add beeswarm plot support to BoxPlot and ViolinPlot (#26)

Bug Fixes

• fix(RidgePlot): drop unused levels from split_by variable
• fix(DimPlot): handle NA values in ordering for high-top and low-top options (pwwang/scplotter#29)
• fix(docs): update link to all available color palettes in basic design vignette

Documentation

• docs: add BeeswarmPlot to the list of available plots in README

Contributors

• @Copilot made their first contribution in #26

Full Changelog: 0.9.0…0.9.1

Version 0.9.0

Bug Fixes

• fix(box/violinplot): comment out error message for group_by comparisons
• fix(boxviolinplot): skip processing for data frames with less than 2 rows
• fix(network): update ggplot2 version check for link_type_by support (#21)
• fix(velocityplot): update ggplot2 version check for arrow length handling (#19, #22)
• chore(heatmap): add warning for unknown arguments in HeatmapAtomic function
• fix(boxviolinplot): make sig_labelsize relative to theme base_size

Documentation

• docs(ROCCurve): update example to include cutoffs_at parameter for clarity

Full Changelog: 0.8.2…0.9.0

Version 0.8.2

Bug Fixes

• fix(prepare_fgsea_result): correct NES NA handling and add print statement
• fix(GSEASummaryPlot): remove debug print statement

Full Changelog: 0.8.1…0.8.2

Version 0.8.1-rc7 (Release Candidate)

New Features

• feat(jitterplot): add order_by parameter for data labeling

Documentation

• chore(jitterplot): use simpler order_by parameter in examples

Full Changelog: 0.8.1-rc6…0.8.1-rc7

Version 0.8.1-rc6 (Release Candidate)

Bug Fixes

• fix(heatmap): preserve the column/row order if given as factor in long form
• fix(volcanoplot): use parameter linewidth for cutoffs instead of deprecated size
• fix(heatmap): optimize data grouping and processing for dot_size
• fix(heatmap): fix default dot size data for flipped plot

Documentation

• docs(heatmap): change example of making row/column annotation thinner to thicker
• docs(volcanoplot): add missing documentation for label_by argument

Full Changelog: 0.8.1-rc5…0.8.1-rc6

Version 0.8.1

New Features

• feat(box/violin): add support for paired observations in Box/Violin plots
• feat(RadarPlot/SpiderPlot): add background color and transparency options and fix radial grid lines across y=0
• feat(boxviolinplot): add support for paired tests
• feat(heatmap): allow setting parameters for name annotations and set default width/height to 2.5mm
• feat(heatmap): enhance dot size functionality to support indexes and dim names
• feat(jitterplot): add order_by parameter for data labeling

Bug Fixes

• fix(dotplot): update color handling in DotPlotAtomic function due to ggplot2 v4
• fix(barplot): correct label positioning and scaling in BarPlotGrouped
• fix(heatmap): prevent double printing in pkgdown with ggplot2 >= 4
• fix(boxviolinplot): enhance pairwise comparison handling when tests fail
• fix(heatmap): update viewport handling for pie and boxviolin layers
• fix(heatmap): prevent double printing in pkgdown with return_grob flag
• fix(heatmap): preserve the column/row order if given as factor in long form
• fix(heatmap): ensure grouping retains all levels
• fix(heatmap): optimize data grouping and processing for dot_size
• fix(heatmap): fix default dot size data for flipped plot

Documentation

• docs(heatmap): change example of making row/column annotation thinner to thicker
• docs(volcanoplot): add missing documentation for label_by argument
• chore(jitterplot): use simpler order_by parameter in examples

Full Changelog: 0.8.0…0.8.1

Version 0.8.1-rc5 (Release Candidate)

New Features

• feat(heatmap): allow setting parameters for name annotations and set default width/height to 2.5mm
• feat(heatmap): enhance dot size functionality to support indexes and dim names

Bug Fixes

• fix(heatmap): update viewport handling for pie and boxviolin layers
• fix(heatmap): prevent double printing in pkgdown with return_grob flag

Full Changelog: 0.8.1-rc4…0.8.1-rc5

Version 0.8.1-rc4 (Release Candidate)

New Features

• feat(box/violin): add support for paired observations in Box/Violin plots
• feat(RadarPlot/SpiderPlot): add background color and transparency options and fix radial grid lines across y=0

Bug Fixes

• fix(dotplot): update color handling in DotPlotAtomic function due to ggplot2 v4
• fix(barplot): correct label positioning and scaling in BarPlotGrouped
• fix(heatmap): prevent double printing in pkgdown with ggplot2 >= 4
• fix(boxviolinplot): enhance pairwise comparison handling when tests fail

Full Changelog: 0.8.0…0.8.1-rc4

Version 0.8.0

Major Announcement

🎆 plotthis is now compatible with ggplot2 v4!

New Features

• feat: add JitterPlot

Bug Fixes

• fix(gsea): handle zero normalization in running enrichment score calculation
• fix(CorPlot): handle when x has zero standard variation (#23)
• fix(Heatmap): update return_grob logic to adopt ggplot2 v4 (#20)
• fix(BarPlot): adjust label_nudge parameter for bar plot functions

Infrastructure

• chore: introduce renv for package dependency management
• chore(dotplot): update examples to avoid testing during documentation build
• chore(Network): handle ggplot2 v4 compatibility for link_type_by
  • Still need thomasp85/ggraph#394 to be fixed to get full support
• chore(VelocityPlot): handle ggplot2 v4 compatibility for arrow lengths
  • Still need tidyverse/ggplot2#6594 to be fixed to get full support

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