Flexible, Interactive 'shiny' Modules for Almost Any Plot

Documentation for package ‘VizModules’ version 0.6.0

Help Pages

-- A --

add_ablines	Build diagonal (abline) line shapes for a plotly figure
add_hlines	Build horizontal line shapes for a plotly figure
add_marginal_plots	Add marginal distribution plots to a scatter plot
add_plot_config	Create default Plotly configuration
add_reference_lines	Add reference lines to a plotly figure from Shiny inputs
add_size_legend	Add a point-size legend to a plotly figure
add_vlines	Build vertical line shapes for a plotly figure
adjusted_axis_label	Build an adjustment-aware axis label
adjusted_values	Transform values the way the modules plot them
adjustment_fn	The whole plotted transform as one function, for dittoViz
adjust_column_values	Adjust numeric column values in a data frame using mathematical transformations
apply_axis_padding	Set the padding between a figure's data and the edges of its plot area
apply_axis_title_to_annotations	Apply axis title font styling to shared facet axis annotations
apply_facet_subplot_spacing	Apply custom subplot spacing to a faceted ggplotly figure
apply_highlight_styling	Restyle highlighted points in a plotly figure
apply_legend_inputs	Apply the uniform Legend inputs to a plotly figure
apply_legend_styling	Apply uniform legend styling to a plotly figure
apply_level_order	Reorder the levels of a categorical column
apply_plotly_newshape	Apply Plotly newshape styling from uniform Plotly inputs
apply_render_margins	Apply standard render-time margin layout to a plotly figure
apply_stat_annotations	Apply statistical annotation shapes and annotations to a plotly figure
apply_subplot_axis_styling	Apply axis styling to all subplot axes in a plotly figure
apply_tick_notation	Set the notation of a figure's numeric tick labels
apply_title_layout	Apply plot title styling to a plotly figure
apply_uniform_styling	Apply the uniform styling inputs to a module's figure
as_plotted	Replace data columns with the values the modules plot for them
auto_webgl	Draw a figure's point layers with WebGL
axis_titles_as_annotations	Convert native cartesian axis titles to draggable annotations

-- B --

blank_to_null	Normalize a module's "no selection" column input to 'NULL'
build_facet_annotations	Build facet subplot annotations
build_facet_panel_borders	Build paper-anchored panel border shapes for a faceted plotly figure
build_model_row_spec	Build a dynamic row_spec from registered backends

-- C --

cached_structure	Cache a module's plot step
clean_facet_dim	Clean and validate facet dimension value for lineplot module
collect_source_data	Collect plot and source data for download
ComplexHeatmap_HeatmapApp	Create an example Modular ComplexHeatmap Shiny Application
ComplexHeatmap_HeatmapInfoOutputUI	Click/brush info output UI component for the ComplexHeatmap module
ComplexHeatmap_HeatmapInputsUI	Input UI components for the ComplexHeatmap module
ComplexHeatmap_HeatmapMainOutputUI	Main heatmap output UI component for the ComplexHeatmap module
ComplexHeatmap_HeatmapOutputUI	Output UI components for the ComplexHeatmap module
ComplexHeatmap_HeatmapServer	Server logic for the ComplexHeatmap module
ComplexHeatmap_HeatmapStaticOutputUI	Static (non-interactive) heatmap output UI component for the ComplexHeatmap module
ComplexHeatmap_HeatmapSubOutputUI	Sub-heatmap output UI component for the ComplexHeatmap module
compute_pairwise_stats	Compute pairwise statistical tests between groups
createModuleApp	Create an Example Module App from Any Module Trio
create_axis_styles	Create Plotly axis style list
create_ggplot_axis_style	Create ggplot axis styling theme arguments
create_highlight_annotations	Create annotations for highlighted points
create_selected_annotations	Create annotations for selected points
create_source_download_handler	Create download handler for plot with source data
create_stat_annotations	Create plotly shapes and annotations for statistical test results

-- D --

dataFilterServer	Server logic for the dataFilter module
dataFilterUI	UI component for the dataFilter module
default_group_colors	Extract a caller-supplied group color mapping from 'defaults'
default_palettes	Color palette options for palettePicker
default_stat_pairs	Pick the comparisons a 'defaults' list asks for from those on offer
discrete_choices	Choices for a categorical colour, shape, group or fill selector
dittoViz_freqPlotApp	Create an example Modular freqPlot Shiny Application
dittoViz_freqPlotInputsUI	Input UI components for the freqPlot module
dittoViz_freqPlotOutputUI	Output UI components for the freqPlot module
dittoViz_freqPlotServer	Server logic for freqPlot module
dittoViz_scatterPlotApp	Create an example Modular scatterPlot Shiny Application
dittoViz_scatterPlotInputsUI	Input UI components for the scatterPlot module
dittoViz_scatterPlotOutputUI	Output UI components for the scatterPlot module
dittoViz_scatterPlotServer	Server logic for scatterPlot module
dittoViz_yPlotApp	Create an example Modular yPlot Shiny Application
dittoViz_yPlotInputsUI	Input UI components for the yPlot module
dittoViz_yPlotOutputUI	Output UI components for the yPlot module
dittoViz_yPlotServer	Server logic for yPlot module
draw_to_png	Render a grid or base drawing to PNG bytes
draw_to_svg	Render a grid or base drawing to a self-contained SVG fragment
dumbbellPlot	Create an Interactive Dumbbell Plot with plotly
dumbbellPlotApp	Create a Shiny App for Dumbbell Plots
dumbbellPlotInputsUI	Input UI components for the dumbbellPlot module
dumbbellPlotOutputUI	Output UI components for the dumbbellPlot module
dumbbellPlotServer	Server logic for dumbbellPlot module

-- E --

empty_plot	Create an empty ggplot2 plot or plotly plot with input text
error_bar_halfwidth	Half-width of a group's error bar
example_bar	Bar dataset for bar and split bar plot examples
example_composition	Example single-cell-style composition data for the freqPlot module
example_demographics	Example demographics dataset
example_heatmap_column_data	Example sample-metadata table for the ComplexHeatmap module
example_heatmap_matrix	Example gene-expression-style matrix for the ComplexHeatmap module
example_iris	Example grouped iris dataset
example_markers	Example single-cell marker gene dataset for dot plots
example_mtcars	Example mtcars dataset with factors
example_population	Example population dataset
example_rnaseq	Example pseudo-bulk RNA-seq dataset
example_sales	Example sales dataset
example_school_earnings	Example school earnings dataset for dumbbell plots
example_skills	Example multi-player skills dataset for radar plots

-- F --

facet_check	Identify columns valid for faceting or splitting
figureBuilderApp	Create a VizModules Figure Builder Application
figureBuilderServer	Server logic for the Figure Builder module
figureBuilderUI	UI component for the Figure Builder module
finalize_manual_edits	Render persistent manual plot layout edits across re-renders
flatten_palette_options	Flatten nested palette options

-- G --

generate_pair_strings	Generate comparison pair strings from data columns
get_default	Resolve a default value from a named list
get_documentation	Extract parameter documentation from an R function help page
get_model_backend	Get a registered model backend

-- H --

heatmap_fit_width	Fit a hand-built InteractiveComplexHeatmap widget to its container's width
hide_input	Hide the grid cells wrapping module inputs

-- I --

is_pure_type

Check if column inputs contain mixed data types

-- L --

level_order_choices	The levels a categorical column is plotted in, optionally reordered
level_order_input	Drag-and-drop control for the order of a categorical axis
linePlot	Create an Interactive Line Plot with plotly
linePlotApp	Create an example Modular linePlot Shiny Application
linePlotInputsUI	Input UI components for the linePlot module
linePlotOutputUI	Output UI components for the linePlot module
linePlotServer	Server logic for linePlot module
linetype_to_dash	Convert linetype name to plotly dash style
list_model_backends	List registered model backends

-- M --

main_title_input_ids	Input IDs that style the main plot title
mark_overlay_axes	Exempt a figure's overlay axes from the shared styling
merge_annotation_sets	Merge two sets of plotly point annotations
moduleGalleryApp	Launch the VizModules module gallery
module_tack_ui	Create standard tack UI for module inputs
multiColorPicker	Compact multi-group color picker input
multiDynamicInput	Dynamic multi-row input for repeating groups of inputs

-- N --

na_to_null	Convert NA or empty string to NULL
note_brackets_skipped	Tell the user why significance brackets are missing from the plot
nz_value	Is an input's value a usable, non-empty string?

-- O --

organize_inputs

Organize arbitrary Shiny inputs into a grid layout

-- P --

parallelCoordinatesPlot	Create an Interactive Parallel Coordinates Plot with plotly
parallelCoordinatesPlotApp	Create an example Modular parallelCoordinatesPlot Shiny Application
parallelCoordinatesPlotInputsUI	Input UI components for the parallelCoordinatesPlot module
parallelCoordinatesPlotOutputUI	Output UI components for the parallelCoordinatesPlot module
parallelCoordinatesPlotServer	Server logic for parallelCoordinatesPlot module
parse_highlight_values	Parse a highlight string into the values it names
parse_numeric_list	Parse comma-separated numeric string to vector
parse_pair_strings	Parse pair strings from UI into list of length-2 vectors
piePlot	Create a plotly pie chart
piePlotApp	Create an example Modular piePlot Shiny Application
piePlotInputsUI	Input UI components for the piePlot module
piePlotOutputUI	Output UI components for the piePlot module
piePlotServer	Server logic for piePlot module
plotthis_AreaPlotApp	Create an example Modular AreaPlot Shiny Application
plotthis_AreaPlotInputsUI	Input UI components for the AreaPlot module
plotthis_AreaPlotOutputUI	Output UI components for the AreaPlot module
plotthis_AreaPlotServer	Server logic for AreaPlot module
plotthis_BarPlotApp	Create an example Modular BarPlot Shiny Application
plotthis_BarPlotInputsUI	Input UI components for the BarPlot module
plotthis_BarPlotOutputUI	Output UI components for the BarPlot module
plotthis_BarPlotServer	Server logic for BarPlot module
plotthis_BoxPlotApp	Create an example Modular BoxPlot Shiny Application
plotthis_BoxPlotInputsUI	Input UI components for the BoxPlot module
plotthis_BoxPlotOutputUI	Output UI components for the BoxPlot module
plotthis_BoxPlotServer	Server logic for BoxPlot module
plotthis_DensityPlotApp	Create an example Modular DensityPlot Shiny Application
plotthis_DensityPlotInputsUI	Input UI components for the DensityPlot module
plotthis_DensityPlotOutputUI	Output UI components for the DensityPlot module
plotthis_DensityPlotServer	Density Plot Server Module
plotthis_DotPlotApp	Create an example Modular DotPlot Shiny Application
plotthis_DotPlotInputsUI	Input UI components for the DotPlot module
plotthis_DotPlotOutputUI	Output UI components for the DotPlot module
plotthis_DotPlotServer	Server logic for DotPlot module
plotthis_HistogramApp	Create an example Modular Histogram Shiny Application
plotthis_HistogramInputsUI	Input UI components for the Histogram module
plotthis_HistogramOutputUI	Output UI components for the histogramPlot module
plotthis_HistogramServer	Histogram Plot Server Module
plotthis_SplitBarPlotApp	Create an example Modular SplitBarPlot Shiny Application
plotthis_SplitBarPlotInputsUI	Input UI components for the SplitBarPlot module
plotthis_SplitBarPlotOutputUI	Output UI components for the SplitBarPlot module
plotthis_SplitBarPlotServer	Server logic for SplitBarPlot module

-- R --

radarPlot	Create a plotly radar chart
radarPlotApp	Create an example Modular radarPlot Shiny Application
radarPlotInputsUI	Input UI components for the radarPlot module
radarPlotOutputUI	Output UI components for the radarPlot module
radarPlotServer	Server logic for radarPlot module
recycle_line_style	Recycle style vector to match line count
register_model_backend	Register a model backend
require_data_frame	Require a data frame from a module's data reactive
reset_annotation_inputs	Reset uniform Annotation inputs to defaults
reset_axes_inputs	Reset uniform axes inputs to defaults
reset_axis_title_text	Drop persisted axis-title text edits
reset_colorscale_inputs	Reset uniform Color Scale inputs to defaults
reset_group_colors	Restore a group color picker to its default mapping
reset_legend_inputs	Reset uniform Legend inputs to defaults
reset_lines_inputs	Reset uniform lines inputs to defaults
reset_manual_edits	Discard every captured manual layout edit
reset_plotly_inputs	Reset uniform Plotly inputs to defaults
reset_stats_inputs	Reset uniform stats inputs to defaults
resolve_colorscale	Resolve a continuous colour scale for plotly
resolve_column_targets	Translate column names or positions into DT column targets
resolve_facet_layout	Resolve number of rows for a faceted subplot grid
resolve_facet_sharing	Resolve facet axis sharing from facet.scales
resolve_palette	Resolve a color palette for plot groups

-- S --

safe_eval_filter	Safely evaluate a user-provided filter expression against a data frame
safe_resolve_adj_fxn	Safely resolve an adjustment function name to an actual function
setup_auto_update_logic	Set up auto-update/isolate logic for reactive contexts
setup_axis_range	Track the axis limits a plot should draw with
setup_group_colors	Track the group-to-color mapping a plot should draw with
setup_level_order	Keep a level-order control in step with its column
setup_manual_edits	Set up persistent manual plot layout edits across re-renders
setup_reactive_defaults	Resolve reactive 'defaults' entries into a server-side parameter store
show_input	Show the grid cells wrapping module inputs
split_color_shape_legend	Give a plot's colour and shape their own legend sections
stat_bracket_headroom	Bracket headroom for a module, read straight off its Stats tab
stat_bracket_y_max	Y-axis top needed to draw statistical annotation brackets in full
string_to_linetypes	Parse and validate linetype string to a vector
subplot_spacing_defaults	Resolve the subplot spacing defaults

-- T --

toggle_facet_title_inputs	Match the title inputs to whether a plot is faceted
toggle_input_cell	Hide or show the grid cell wrapping a module input

-- U --

uniform_annotation_inputs_ui	Generate uniform Annotation input UI
uniform_axes_inputs_ui	Generate uniform Axes input UI
uniform_colorscale_inputs_ui	Generate uniform Color Scale input UI
uniform_legend_inputs_ui	Generate uniform Legend input UI
uniform_lines_inputs_ui	Generate uniform Lines input UI
uniform_plotly_inputs_ui	Generate uniform Plotly input UI
uniform_stats_inputs_ui	Generate uniform Stats input UI
uniform_subplot_spacing_inputs_ui	Generate uniform subplot spacing input UI
updateMultiColorPicker	Update a multiColorPicker input on the client
updateMultiDynamicInput	Update a multiDynamicInput input on the client
update_viz_select	Update a select input created by viz_select_input
use_vizmodules_skills	Install the bundled VizModules agent skills into a project

-- V --

validate_expression	Validate a user-provided expression string for safety
viz_select_input	Create a select input that scales to very large choice sets

-- W --

webgl_input	The "Plot with WebGL" toggle for a module's point layers
with_stable_seed	Evaluate a plot expression under a fixed random seed