Skip to contents

Input UI components for the BoxPlot module

Source: R/plotthis_BoxPlot_module_ui.R
plotthis_BoxPlotInputsUI.Rd

This should be placed in the UI where the inputs should be shown, with an id that matches the id used in the plotthis_BoxPlotServer() and plotthis_BoxPlotOutputUI() functions.

Usage

plotthis_BoxPlotInputsUI(id, data, defaults = NULL, title = NULL, columns = 2)

Arguments

id

The ID for the Shiny module.

data

The data frame used for plot generation.

defaults

A named list of default values for the inputs. An entry may also be a shiny::reactive() or shiny::reactiveVal(); it is resolved with shiny::isolate() to seed the control, and the module then keeps it live (see setup_reactive_defaults()).

title

An optional title for the UI grid.

columns

Number of columns for the UI grid.

Value

A Shiny tagList containing the UI elements

Details

The user inputs for this module are separated from the outputs to allow for more flexible UI design.

The inputs will automatically be organized into a grid layout via the organize_inputs() function, with columns controlling the number of columns in the grid.

Defaults can be set for each input by providing a named list of values to the defaults argument. Nearly all parameters for plotthis::BoxPlot() can be set via these inputs, so see the help for that function for an exhaustive list.

Plot parameters not implemented or with altered functionality

The following plotthis::BoxPlot() parameters are not available via UI inputs:

  • xlab - X-axis label (plotly allows interactive editing)

  • ylab - Y-axis label (plotly allows interactive editing)

  • title - Plot title (plotly allows interactive editing)

  • subtitle - Plot subtitle (not supported in plotly)

  • aspect.ratio - Aspect ratio control (handled by plotly layout)

  • legend.position - Legend positioning (plotly allows interactive repositioning)

  • x_sep - Separator for x columns (not applicable in UI context)

  • in_form - Data input format (not applicable - always long form)

  • split_by - Split variable (returns a patchwork object, not supported in plotly), use facet_by instead

  • split_by_sep - Only applies if split_by is used

  • symnum_args - Significance symbol arguments (the Stats tab manages symbol display)

  • keep_empty - Keep empty values (not implemented)

  • keep_na - Keep NA values (not implemented)

  • group_by_sep - Separator for group columns (not applicable in UI context)

  • group_name - Group legend name (handled by plotly)

  • paired_by - Pairing variable for paired tests (use the Stats tab "Paired Test" input instead)

  • x_text_angle - X-axis text angle (handled by plotly axis settings)

  • step_increase - Step increase for significance brackets (set via the Stats tab "Bracket Spacing")

  • base - Base plot type box/violin/bar (fixed to "box" in this module)

  • fill_mode - Fill mode for grouped data (handled automatically)

  • position_dodge_preserve - Preserve dodge width (not implemented)

  • add_errorbar - Add error bars (only for base = "bar"; not implemented)

  • errorbar_color - Error bar color (not implemented)

  • errorbar_width - Error bar cap width (not implemented)

  • errorbar_linewidth - Error bar line width (not implemented)

  • theme - ggplot2 theme (not applicable in plotly)

  • theme_args - Theme arguments (not applicable in plotly)

  • palette - Managed internally via the palette selection UI

  • palreverse - Reverse the color palette (not implemented)

  • alpha - Alpha transparency (not implemented in UI)

  • stack - Stack boxplots (not implemented)

  • add_beeswarm - Add beeswarm points (not implemented in UI)

  • beeswarm_method - Beeswarm arrangement method (not implemented)

  • beeswarm_cex - Beeswarm point size factor (not implemented)

  • beeswarm_priority - Beeswarm priority order (not implemented)

  • beeswarm_dodge - Beeswarm dodge width (not implemented)

  • add_trend - Add trend line (not implemented in UI)

  • trend_color - Trend line color (not implemented)

  • trend_linewidth - Trend line width (not implemented)

  • trend_ptsize - Trend point size (not implemented)

  • add_stat - Add statistical annotation (not implemented)

  • stat_name - Statistical test name (not implemented)

  • stat_color - Statistical annotation color (not implemented)

  • stat_size - Statistical annotation size (not implemented)

  • stat_stroke - Statistical annotation stroke (not implemented)

  • stat_shape - Statistical annotation shape (not implemented)

  • add_bg - Add background shading (not implemented)

  • bg_palette - Background palette (not implemented)

  • bg_palcolor - Background color (not implemented)

  • bg_alpha - Background transparency (not implemented)

  • add_line - Add horizontal line (not implemented in UI - use Lines tab)

  • line_color - Line color (not implemented)

  • line_width - Line width (not implemented)

  • line_type - Line type (not implemented)

  • comparisons - plotthis pairwise comparisons are not passed; equivalent pairwise significance testing is provided via the module's Stats tab (see "Statistical annotation parameters")

  • ref_group - Reference group for comparisons (use the Stats tab instead)

  • pairwise_method - Pairwise test method (set via the Stats tab "Test" input instead)

  • multiplegroup_comparisons - Multiple-group comparison flag (use the Stats tab instead)

  • multiple_method - Multiple-group test method (set via the Stats tab "Test" input instead)

  • sig_label - Significance label format (set via the Stats tab "Display" input instead)

  • sig_labelsize - Significance label size (handled by the Stats tab)

  • hide_ns - Hide non-significant comparisons (use the Stats tab "Hide Non-Significant" input)

  • seed - Random seed (not applicable)

  • combine - Only applies if split_by is used

  • nrow - Only applies if split_by is used

  • ncol - Only applies if split_by is used

  • byrow - Only applies if split_by is used

  • axes - Only applies if split_by is used

  • axis_titles - Only applies if split_by is used

  • guides - Only applies if split_by is used

  • legend.direction - Managed position of legend however this can be handled via plotly

Plot parameters and defaults

The following plotthis::BoxPlot() parameters can be accessed via UI inputs and/or the defaults argument:

  • x - X-axis variable (UI: "X data", default: 2nd categorical variable)

  • y - Y-axis variable (UI: "Y data", default: 2nd numeric variable)

  • group_by - Grouping variable (UI: "Group by", default: "")

  • flip - Flip/swap the x and y axes (UI: "Rotate (swap X/Y)", default: FALSE)

  • sort_x - Sort X-axis by statistic (UI: "Sort X by", default: ""). An expression evaluated once per x group over all the data, e.g. mean(salary); a faceted plot shares the one order across its panels

  • y_max - Maximum Y-axis value (UI: "Max Value of Y Axis", default: calculated)

  • y_min - Minimum Y-axis value (UI: "Min Value of Y Axis", default: calculated)

  • add_point - Add jitter points (UI: "Add Jitter Points", default: FALSE)

  • pt_size - Point size (UI: "Point Size", default: 1)

  • pt_alpha - Point transparency (UI: "Point Alpha", default: 1)

  • jitter_width - Jitter width (UI: "Jitter Width", default: 0.3)

  • pt_color - Point outline color (UI: "Point Outline Colour", default: "#000000")

  • highlight - Highlight condition (UI: "Highlight", default: "")

  • highlight_color - Highlight color (UI: "Highlight Colour", default: "#000000")

  • highlight_size - Highlight size (UI: "Highlight Size", default: 1)

  • highlight_alpha - Highlight transparency (UI: "Highlight Alpha", default: 1)

  • facet_by - Faceting variable (UI: "Facet by", default: "")

  • facet_scales - Facet scale behavior (UI: "Facet Scale", default: "fixed")

  • facet_ncol - Number of facet columns (UI: "Columns", default: NULL)

  • facet_nrow - Number of facet rows (UI: "Rows", default: NULL)

  • facet_byrow - Facet ordering direction (UI: "Facet by Row", default: TRUE)

  • palcolor - Custom color values (UI: palette picker, derived from palette)

Statistical annotation parameters

The module provides plotly-based significance testing via the Stats tab (a reimplementation of the plotthis significance-testing features). The following inputs are available:

  • stats.enabled - Enable statistical annotations (UI: "Enable Stats", default: FALSE)

  • stat.test - Test to apply: Wilcoxon, t-test, Kruskal-Wallis, or ANOVA (UI: "Test")

  • stat.p.adjust - P-value adjustment method (UI: "P-value Adjustment", default: "holm")

  • stat.display - Value to display: adjusted p-value, p-value, or symbols (UI: "Display")

  • stat.sig.threshold - Significance threshold for symbols/hiding (UI: "Significance Threshold")

  • stat.hide.ns - Hide non-significant comparisons (UI: "Hide Non-Significant", default: TRUE)

  • stat.paired - Use a paired test (UI: "Paired Test", default: FALSE)

  • stat.pairs - Group comparisons to test (UI: "Comparisons", multiple selection, default: all pairs). As a default, a character vector of "A vs B" strings naming levels of x.data (or of group.by, when set), e.g. c("Entry vs Mid", "Mid vs Senior"); either order matches

  • stat.line.color - Bracket line color (UI: "Line Color", default: "#000000")

  • stat.line.width - Bracket line width (UI: "Line Width")

  • stat.bracket.style - Bracket style, capped or flat (UI: "Bracket Style")

  • stat.step.increase - Vertical spacing between stacked brackets (UI: "Bracket Spacing")

  • stat.text.bump - Offset of the significance text above the bracket (UI: "Text Offset")

  • stat.bracket.inset - Horizontal inset of the brackets (UI: "Bracket Inset")

  • stat.per.facet - Compute statistics independently per facet panel (UI: "Per Facet Panel")

Brackets are stacked above the data, so none are drawn while the plot is rotated (the values then run along the x-axis); the test results are still included in the source data download. Under a free y facet scale ("free", "free_y") each panel's brackets sit above that panel's own data, and the Y axis min/max are not applied.

Parameters controlling additional functionality

The following parameters implementing new functionality or controlling plotly-specific features are also available:

  • webgl - Draw the points with WebGL once there are 5,000 or more, as set by the VizModules.webgl.threshold option (UI: "Plot with WebGL", default: TRUE)

  • boxplot.width - Width of boxplot (UI: "Boxplot Width", default: 0.8)

  • x.order - Order of the X groups (UI: "X Order", drag and drop, default: the column's factor level order, else sorted). As a default, a character vector of levels of x.data; levels it leaves out follow in their default order. Ignored while sort_x is set, and not shown for an X with more than 20 groups

  • show.outliers - Show outlier points (UI: "Show Outliers", default: TRUE)

  • axis.title.font.size - Axis title font size (UI: "Axis title size", default: 18)

  • title.font.size - Plot title font size (UI: "Title Size", default: 26)

  • title.font.family - Font family for title text (UI: "Title Font", default: "Arial")

  • title.font.color - Color for plot title (UI: "Title Color", default: "#000000")

  • axis.title.font.size - Axis title font size (UI: "Axis Title Size", default: 18)

  • axis.title.font.color - Axis title font color (UI: "Axis Title Color", default: "#000000")

  • axis.title.font.family - Axis title font family (UI: "Axis Title Font", default: "Arial")

  • axis.showline - Show axis border lines (UI: "Show axis lines", default: TRUE)

  • axis.mirror - Mirror axis lines on opposite side (UI: "Mirror axis lines", default: TRUE)

  • show.grid.x - Show X-axis major gridlines (UI: "Show X major gridlines", default: TRUE)

  • show.grid.y - Show Y-axis major gridlines (UI: "Show Y major gridlines", default: TRUE)

  • axis.linecolor - Color of axis lines (UI: "Axis line color", default: "black")

  • axis.linewidth - Width of axis lines (UI: "Axis line width", default: 0.5)

  • axis.tickfont.size - Size of tick labels (UI: "Tick label size", default: 12)

  • axis.tickfont.color - Color of tick labels (UI: "Tick label color", default: "black")

  • axis.tickfont.family - Font family for tick labels (UI: "Tick label font", default: "Arial")

  • axis.tickangle.x - Rotation angle for X-axis tick labels (UI: "X-axis tick label angle", default: 0)

  • axis.tickangle.y - Rotation angle for Y-axis tick labels (UI: "Y-axis tick label angle", default: 0)

  • axis.ticks - Position of tick marks (UI: "Tick position", default: "outside")

  • axis.tickcolor - Color of tick marks (UI: "Tick mark color", default: "black")

  • axis.ticklen - Length of tick marks (UI: "Tick mark length", default: 5)

  • axis.tickwidth - Width of tick marks (UI: "Tick mark width", default: 1)

  • axis.scientific - Write numeric tick labels in scientific notation (UI: "Scientific Notation Ticks", default: FALSE; when off they never switch to it). See apply_tick_notation()

  • axis.padding.x - Space between the data and the plot area's edges along X, as a fraction of the data's extent at each end (UI: "X Axis Padding", default: NA = the plot's own). See apply_axis_padding()

  • legend.show - Show the legend and any colorbar (UI: "Show Legend", default: TRUE)

  • legend.font.family - Font family of the legend title and labels (UI: "Legend Font", default: "Arial")

  • legend.font.color - Font color of the legend title and labels (UI: "Legend Font Color", default: "#000000")

  • legend.title.size - Legend title font size (UI: "Legend Title Size", default: 14)

  • legend.text.size - Legend entry label font size (UI: "Legend Text Size", default: 12)

  • hline.intercepts - Y-coordinates for horizontal reference lines (UI: "Y-intercepts", default: "")

  • hline.colors - Colors for horizontal lines (UI: "Colors", default: "#000000")

  • hline.widths - Widths for horizontal lines (UI: "Widths", default: "1")

  • hline.linetypes - Line types for horizontal lines (UI: "Line types", default: "dashed")

  • hline.opacities - Opacities for horizontal lines (UI: "Opacities (0-1)", default: "1")

  • vline.intercepts - X-coordinates for vertical reference lines (UI: "X-intercepts", default: "")

  • vline.colors - Colors for vertical lines (UI: "Colors", default: "#000000")

  • vline.widths - Widths for vertical lines (UI: "Widths", default: "1")

  • vline.linetypes - Line types for vertical lines (UI: "Line types", default: "dashed")

  • vline.opacities - Opacities for vertical lines (UI: "Opacities (0-1)", default: "1")

  • abline.slopes - Slopes for diagonal reference lines (UI: "Slopes", default: "")

  • abline.intercepts - Y-intercepts for diagonal lines (UI: "Y-intercepts", default: "")

  • abline.colors - Colors for diagonal lines (UI: "Colors", default: "#000000")

  • abline.widths - Widths for diagonal lines (UI: "Widths", default: "1")

  • abline.linetypes - Line types for diagonal lines (UI: "Line types", default: "dashed")

  • abline.opacities - Opacities for diagonal lines (UI: "Opacities (0-1)", default: "1")

  • palette.colours - Named character vector mapping group levels to colors, e.g. c(A = "#FF0000", B = "blue") (UI: "Plot colors"). Seeds the picker; unnamed groups fall back to the default palette and user edits take precedence.

See also

plotthis::BoxPlot(), organize_inputs(), plotthis_BoxPlotOutputUI(), plotthis_BoxPlotServer(), plotthis_BoxPlotApp()

Author

Jacob Martin, Jared Andrews

Examples

if (FALSE) { # interactive()
library(VizModules)
data(mtcars)
plotthis_BoxPlotInputsUI("BoxPlot", mtcars)
}