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Input UI components for the ViolinPlot module

Source: R/plotthis_ViolinPlot_module_ui.R
plotthis_ViolinPlotInputsUI.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_ViolinPlotServer() and plotthis_ViolinPlotOutputUI() functions.

Usage

plotthis_ViolinPlotInputsUI(
  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.

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::ViolinPlot() 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::ViolinPlot() 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 (not implemented)

  • flip - Flip axes (not implemented in current UI)

  • 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 (not implemented)

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

  • step_increase - Step increase for significance brackets (not implemented)

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

  • fill_reverse - Reverse fill order (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

  • alpha - Alpha transparency (not implemented in UI)

  • stack - Stack violins (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 - Group comparisons for significance tests (not implemented)

  • ref_group - Reference group for comparisons (not implemented)

  • pairwise_method - Pairwise test method (not implemented)

  • multiplegroup_comparisons - Multiple group comparison flag (not implemented)

  • multiple_method - Multiple group test method (not implemented)

  • sig_label - Significance label format (not implemented)

  • sig_labelsize - Significance label size (not implemented)

  • hide_ns - Hide non-significant comparisons (not implemented)

  • 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::ViolinPlot() 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: "")

  • sort_x - Sort X-axis by statistic (UI: "Sort X By", default: "none")

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

  • y_min - Minimum Y-axis value (UI: "Y Min", 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: 0.5)

  • jitter_height - Jitter height (UI: "Jitter Height", default: 0)

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

  • add_box - Add box plot overlay (UI: "Add Box", default: FALSE)

  • box_color - Box outline color (UI: "Box Colour", default: "#000000")

  • box_width - Box width (UI: "Box Width", default: 0.1)

  • box_ptsize - Box point size (UI: "Box Point Size", default: 2.5)

  • 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)

Parameters controlling additional functionality

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

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

  • title.font.size - Plot title font size (UI: "Title font size", default: 28)

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

  • text.colour - Color for axis labels (UI: "Label colour", default: "#000000")

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

  • show.major.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)

  • 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")

See also

plotthis::ViolinPlot(), organize_inputs(), plotthis_ViolinPlotOutputUI(), plotthis_ViolinPlotServer(), plotthis_ViolinPlotApp()

Author

Jacob Martin, Jared Andrews

Examples

library(VizModules)
data(mtcars)
plotthis_ViolinPlotInputsUI("ViolinPlot", mtcars)
#> <div class="tabbable">
#>   <ul class="nav nav-tabs shiny-tab-input" id="ViolinPlot-ViolinPlotTabsetPanel" data-tabsetid="9447">
#>     <li class="active">
#>       <a href="#tab-9447-1" data-toggle="tab" data-bs-toggle="tab" data-value="Data">Data</a>
#>     </li>
#>     <li>
#>       <a href="#tab-9447-2" data-toggle="tab" data-bs-toggle="tab" data-value="Adjustments">Adjustments</a>
#>     </li>
#>     <li>
#>       <a href="#tab-9447-3" data-toggle="tab" data-bs-toggle="tab" data-value="Highlight">Highlight</a>
#>     </li>
#>     <li>
#>       <a href="#tab-9447-4" data-toggle="tab" data-bs-toggle="tab" data-value="Facet">Facet</a>
#>     </li>
#>     <li>
#>       <a href="#tab-9447-5" data-toggle="tab" data-bs-toggle="tab" data-value="Axes">Axes</a>
#>     </li>
#>     <li>
#>       <a href="#tab-9447-6" data-toggle="tab" data-bs-toggle="tab" data-value="Lines">Lines</a>
#>     </li>
#>   </ul>
#>   <div class="tab-content" data-tabsetid="9447">
#>     <div class="tab-pane active" data-value="Data" id="tab-9447-1">
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-x.data-label" for="ViolinPlot-x.data">X Data</label>
#>             <div>
#>               <select id="ViolinPlot-x.data" class="shiny-input-select"><option value=""></option></select>
#>               <script type="application/json" data-for="ViolinPlot-x.data">{"plugins":["selectize-plugin-a11y"]}</script>
#>             </div>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-y.data-label" for="ViolinPlot-y.data">Y Data</label>
#>             <div>
#>               <select id="ViolinPlot-y.data" class="shiny-input-select"><option value=""></option>
#> <option value="mpg" selected>mpg</option>
#> <option value="cyl">cyl</option>
#> <option value="disp">disp</option>
#> <option value="hp">hp</option>
#> <option value="drat">drat</option>
#> <option value="wt">wt</option>
#> <option value="qsec">qsec</option>
#> <option value="vs">vs</option>
#> <option value="am">am</option>
#> <option value="gear">gear</option>
#> <option value="carb">carb</option></select>
#>               <script type="application/json" data-for="ViolinPlot-y.data">{"plugins":["selectize-plugin-a11y"]}</script>
#>             </div>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-group.by-label" for="ViolinPlot-group.by">Group By</label>
#>             <div>
#>               <select id="ViolinPlot-group.by" class="shiny-input-select"><option value="" selected></option>
#> <option value="" selected></option></select>
#>               <script type="application/json" data-for="ViolinPlot-group.by">{"plugins":["selectize-plugin-a11y"]}</script>
#>             </div>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div id="ViolinPlot-palette.selection" class="shiny-html-output"></div>
#>         </div>
#>       </div>
#>     </div>
#>     <div class="tab-pane" data-value="Adjustments" id="tab-9447-2">
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-sort_x-label" for="ViolinPlot-sort_x">Sort X By</label>
#>             <div>
#>               <select id="ViolinPlot-sort_x" class="shiny-input-select"><option value="none" selected>none</option>
#> <option value="mean_asc">mean_asc</option>
#> <option value="mean_desc">mean_desc</option>
#> <option value="mean">mean</option>
#> <option value="median_asc">median_asc</option>
#> <option value="median_desc">median_desc</option>
#> <option value="median">median</option></select>
#>               <script type="application/json" data-for="ViolinPlot-sort_x" data-nonempty="">{"plugins":["selectize-plugin-a11y"]}</script>
#>             </div>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-y.max-label" for="ViolinPlot-y.max">Y Max</label>
#>             <input id="ViolinPlot-y.max" type="number" class="shiny-input-number form-control" value="37.629" data-update-on="change"/>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-y.min-label" for="ViolinPlot-y.min">Y Min</label>
#>             <input id="ViolinPlot-y.min" type="number" class="shiny-input-number form-control" value="10.4" data-update-on="change"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <div class="material-switch">
#>               <label for="ViolinPlot-add.points" style="padding-right: 10px;">Add Jitter Points</label>
#>               <input id="ViolinPlot-add.points" type="checkbox"/>
#>               <label class="switch label-success bg-success" for="ViolinPlot-add.points"></label>
#>             </div>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-pt.size-label" for="ViolinPlot-pt.size">Point Size</label>
#>             <input id="ViolinPlot-pt.size" type="number" class="shiny-input-number form-control" value="1" data-update-on="change" min="0.1" max="100"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-pt.alpha-label" for="ViolinPlot-pt.alpha">Point Alpha</label>
#>             <input id="ViolinPlot-pt.alpha" type="number" class="shiny-input-number form-control" value="1" data-update-on="change" min="0" max="1"/>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-jitter.width-label" for="ViolinPlot-jitter.width">Jitter Width</label>
#>             <input id="ViolinPlot-jitter.width" type="number" class="shiny-input-number form-control" value="0.5" data-update-on="change" min="0" max="1"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-jitter.height-label" for="ViolinPlot-jitter.height">Jitter Height</label>
#>             <input id="ViolinPlot-jitter.height" type="number" class="shiny-input-number form-control" value="0" data-update-on="change" min="0" max="1"/>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container" data-shiny-input-type="colour">
#>             <label class="control-label" for="ViolinPlot-pt.color">Point Outline Colour</label>
#>             <input id="ViolinPlot-pt.color" type="text" class="form-control shiny-colour-input" data-init-value="#000000" data-show-colour="both" data-palette="square"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <div class="material-switch">
#>               <label for="ViolinPlot-add.box" style="padding-right: 10px;">Add Box</label>
#>               <input id="ViolinPlot-add.box" type="checkbox"/>
#>               <label class="switch label-success bg-success" for="ViolinPlot-add.box"></label>
#>             </div>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container" data-shiny-input-type="colour">
#>             <label class="control-label" for="ViolinPlot-box.color">Box Colour</label>
#>             <input id="ViolinPlot-box.color" type="text" class="form-control shiny-colour-input" data-init-value="#000000" data-show-colour="both" data-palette="square"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-box.width-label" for="ViolinPlot-box.width">Box Width</label>
#>             <input id="ViolinPlot-box.width" type="number" class="shiny-input-number form-control" value="0.1" data-update-on="change" min="0" max="1"/>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-box.ptsize-label" for="ViolinPlot-box.ptsize">Box Point Size</label>
#>             <input id="ViolinPlot-box.ptsize" type="number" class="shiny-input-number form-control" value="2.5" data-update-on="change" min="0" max="10"/>
#>           </div>
#>         </div>
#>       </div>
#>     </div>
#>     <div class="tab-pane" data-value="Highlight" id="tab-9447-3">
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-highlight-label" for="ViolinPlot-highlight">Highlight</label>
#>             <input id="ViolinPlot-highlight" type="text" class="shiny-input-text form-control" value="" placeholder="E.g. y &gt; 0" data-update-on="change"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container" data-shiny-input-type="colour">
#>             <label class="control-label" for="ViolinPlot-highlight.colour">Highlight Colour</label>
#>             <input id="ViolinPlot-highlight.colour" type="text" class="form-control shiny-colour-input" data-init-value="#000000" data-show-colour="both" data-palette="square"/>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-highlight.size-label" for="ViolinPlot-highlight.size">Highlight Size</label>
#>             <input id="ViolinPlot-highlight.size" type="number" class="shiny-input-number form-control" value="1" data-update-on="change" min="0"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-highlight.alpha-label" for="ViolinPlot-highlight.alpha">Highlight Alpha</label>
#>             <input id="ViolinPlot-highlight.alpha" type="number" class="shiny-input-number form-control" value="1" data-update-on="change" min="0" max="1"/>
#>           </div>
#>         </div>
#>       </div>
#>     </div>
#>     <div class="tab-pane" data-value="Facet" id="tab-9447-4">
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-facet.by-label" for="ViolinPlot-facet.by">Facet By</label>
#>             <div>
#>               <select id="ViolinPlot-facet.by" class="shiny-input-select"><option value="" selected></option>
#> <option value="" selected></option></select>
#>               <script type="application/json" data-for="ViolinPlot-facet.by">{"plugins":["selectize-plugin-a11y"]}</script>
#>             </div>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-facet.scale-label" for="ViolinPlot-facet.scale">Facet Scale</label>
#>             <div>
#>               <select id="ViolinPlot-facet.scale" class="shiny-input-select"><option value="fixed" selected>fixed</option>
#> <option value="free">free</option>
#> <option value="free_x">free_x</option>
#> <option value="free_y">free_y</option></select>
#>               <script type="application/json" data-for="ViolinPlot-facet.scale" data-nonempty="">{"plugins":["selectize-plugin-a11y"]}</script>
#>             </div>
#>           </div>
#>         </div>
#>       </div>
#>       <div class="row">
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-facet.ncol-label" for="ViolinPlot-facet.ncol">Columns</label>
#>             <input id="ViolinPlot-facet.ncol" type="number" class="shiny-input-number form-control" data-update-on="change" min="0"/>
#>           </div>
#>         </div>
#>         <div class="col-sm-6">
#>           <div class="form-group shiny-input-container">
#>             <label class="control-label" id="ViolinPlot-facet.nrow-label" for="ViolinPlot-facet.nrow">Rows</label>
#>             <input id="ViolinPlot-facet.nrow" type="number" class="shiny-input-number form-control" data-update-on="change" min="0"/>
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#> <br/>