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