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Input UI components for the yPlot module

Source: R/dittoViz_yPlot_module_ui.R
dittoViz_yPlotInputsUI.Rd

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

Usage

dittoViz_yPlotInputsUI(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 dittoViz::yPlot() can be set via these inputs, so see the help for that function for an exhaustive list.

The "Y Data" input accepts several columns at once. "Multivar Aesthetic" (on the Facet tab) then decides how they are shown: "split" gives each variable its own facet (alongside any split.by facets), while "group" and "color" put the variables on the x-axis or the fill legend respectively. With several variables the Stats tab is only available for the "split" aesthetic with no split.by set, and comparisons are then run separately within each variable's facet. The other layouts either replace the x-axis groups being compared or facet on two dimensions at once, neither of which the significance brackets can be placed against.

The "Y Adjustment Function" is applied first and the "Y Adjustment" then rescales the result (e.g. log10, then z-score), the reverse of the order dittoViz::yPlot() applies its var.adj.fxn and var.adjustment in.

Statistics are computed on the values as plotted, after any Y adjustment, and the Y Axis Min/Max and significance brackets are in those units too. With a ridge plot among the plot types the values run along the x-axis, so no brackets are drawn; the test results are still included in the source data download.

Plot parameters not implemented or with altered functionality

The following dittoViz::yPlot() parameters are not available via UI inputs:

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

  • ylab - Y-axis label (auto-generated to reflect any applied Y adjustment, e.g. "z-score(log2(units))"; plotly allows interactive editing). With several Y variables only the adjustment is shown, as the variables are named by the facet strips or the legend instead

  • main - Plot title (plotly allows interactive editing)

  • sub - Plot subtitle (not supported in plotly)

  • theme - ggplot2 theme (not applicable to plotly)

  • legend.title - Legend title (managed by plotly interactively)

  • add.line - Use hline.intercepts instead for horizontal lines with full styling options

  • line.linetype - Use hline.linetypes instead

  • line.color - Use hline.colors instead

  • line.linewidth - Use hline.widths instead

  • line.opacity - Use hline.opacities instead

  • rows.use - Row subset to plot (not implemented)

  • colors - Integer index/order into color.panel (managed via the palette UI)

  • shape.panel - Shapes used with shape.by (not implemented)

  • y.breaks - Custom continuous-axis breaks (not implemented)

  • x.labels - Override group labels (not implemented)

  • x.labels.rotate - Rotate group labels (handled by the Axes tab tick-angle controls)

  • x.reorder - Reorder x-axis groups (use x.order, the "Group Order" input, instead)

  • boxplot.width - Boxplot width (controlled via boxgap and boxgroupgap)

  • boxplot.outlier.size - Outlier point size (not implemented)

  • boxplot.position.dodge - Boxplot dodge (controlled via boxgap)

  • vlnplot.quantiles - Violin quantiles (doesn't translate to plotly)

Plot parameters and defaults

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

  • var - Y-axis variable(s) (UI: "Y Data", default: 2nd numeric variable). Several may be selected; multivar.aes then controls how they are displayed

  • multivar.aes - Aesthetic used for multiple var columns (UI: "Multivar Aesthetic", default: "split")

  • multivar.split.dir - Facet direction for multiple var columns (UI: "Multivar Split Dir", default: "col")

  • group.by - Grouping variable for x-axis (UI: "Group by", default: 2nd categorical variable)

  • color.by - Coloring variable (UI: "Color by", default: "")

  • shape.by - Shape variable (UI: "Shape by", default: "")

  • split.by - Faceting variable (UI: "Split by (facet)", default: "")

  • plots - Plot types to show (UI: "Plots to show", default: c("boxplot", "jitter"))

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

  • min - Y-axis minimum, in the units plotted (after any var.adjustment/var.adj.fxn); set with the y.min key (UI: "Y Axis Min", auto-calculated). Not applied under a free y facet scale, where each panel spans its own data.

  • max - Y-axis maximum, in the units plotted; set with the y.max key (UI: "Y Axis Max", auto-calculated). Not applied under a free y facet scale.

  • var.adjustment - Y-axis data adjustment (UI: "Y Adjustment", default: "")

  • var.adj.fxn - Y-axis adjustment function (UI: "Y Adjustment Function", default: "")

  • split.nrow - Number of facet rows (UI: "Rows", default: 4)

  • split.ncol - Number of facet columns (UI: "Columns", default: 4)

  • split.adjust - Facet scale behavior (UI: "Facet Scaling", default: "fixed"). A free y scale ("free", "free_y") ignores Y Axis Min/Max and stacks each panel's significance brackets above that panel's own data.

  • do.raster - Rasterize jitter points (UI: "Rasterize Jitter", default: FALSE)

  • raster.dpi - DPI for rasterization (UI: "Raster DPI", default: 600)

  • jitter.size - Jitter point size (UI: "Jitter Point Size", default: 1)

  • jitter.width - Jitter width (UI: "Jitter Width", default: 0.2)

  • jitter.color - Jitter border color (UI: "Jitter Border Color", default: "#000000")

  • jitter.shape.legend.size - Shape legend size (UI: "Shape Legend Size", default: 5)

  • jitter.shape.legend.show - Show shape legend (UI: "Show Shape Legend", default: TRUE)

  • jitter.position.dodge - Jitter position dodge (calculated from boxgap)

  • boxplot.show.outliers - Show boxplot outliers

  • boxplot.color - Boxplot outline color (UI: "Boxplot Color", default: "#000000")

  • boxplot.fill - Fill boxplot (UI: "Fill Boxplot", default: TRUE)

  • boxplot.lineweight - Boxplot line weight (UI: "Boxplot Line Weight", default: 0.5)

  • vlnplot.lineweight - Violin line weight (UI: "Violin Line Weight", default: 0.5)

  • vlnplot.scaling - Violin scaling method (UI: "Violin Scaling", default: "area")

  • vlnplot.width - Violin width (derived from boxgap; not directly settable)

  • ridgeplot.lineweight - Ridge line weight (UI: "Ridge Line Weight", default: 0.5)

  • ridgeplot.scale - Ridge overlap scale (UI: "Ridge Scale (overlap)", default: 1.25)

  • ridgeplot.ymax.expansion - Ridge Y-max expansion (UI: "Ridge Y-max Expansion", default: NA)

  • ridgeplot.shape - Ridge shape (UI: "Ridge Shape", default: "smooth")

  • ridgeplot.bins - Ridge bins (UI: "Ridge Bins", default: 30)

  • ridgeplot.binwidth - Ridge binwidth (UI: "Ridge Binwidth", default: NULL)

  • hover.data - Columns shown on hover (UI: "Hover Data", default: ""; empty uses a sensible default set of columns)

  • hover.round.digits - Hover value rounding (UI: "Hover Round Digits", default: 5)

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

  • stats.enabled and the other stat.* parameters - Pairwise testing between the group.by groups, or between the color.by levels within each group when color.by is set (Stats tab). stat.pairs takes a character vector of "A vs B" strings naming those levels, e.g. "Office vs Remote"; left unset, every pair is tested

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)

  • x.order - Order of the group.by groups along the x-axis (UI: "Group Order", drag and drop, default: the column's factor level order, else sorted). As a default, a character vector of levels of group.by; levels it leaves out follow in their default order. Not shown for a group.by with more than 20 groups

  • boxmode - Always "overlay": the boxes carry explicit x positions matching ggplot's dodge, so plotly.js is not asked to dodge them

  • boxgap - Boxplot position dodge (UI: "Boxplot Position Dodge", default: 0.3)

  • boxgroupgap - Boxplot group dodge (UI: "Boxplot Group Dodge", default: 0.2)

  • 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.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.

  • annotate.by - Column whose values identify and label jitter points (UI: "Annotate By", default: "")

  • highlight.points - Values from the annotate.by column to highlight (UI: "Points to Highlight", default: ""). Values containing spaces (e.g. "CD4 T") must be separated by commas or new lines

  • highlight.color - Fill color for highlighted points (UI: "Highlight Fill", default: "#00FFF7")

  • highlight.size - Size of highlighted points (UI: "Highlight Size", default: 7)

  • highlight.border.color - Border color for highlighted points (UI: "Highlight Border Color", default: "#000000")

  • highlight.border.width - Border width for highlighted points (UI: "Highlight Border Width", default: 1)

  • highlight.auto.annotate - Label highlighted points automatically (UI: "Auto-annotate Highlights", default: TRUE)

  • annotation.color - Annotation text color (UI: "Annotation Color", default: "black")

  • annotation.ax - Horizontal label offset in pixels (UI: "Annotation X Offset", default: 20)

  • annotation.ay - Vertical label offset in pixels (UI: "Annotation Y Offset", default: -20)

  • annotation.size - Annotation font size (UI: "Annotation Size", default: 10)

  • annotation.showarrow - Draw an arrow from label to point (UI: "Show Arrow", default: TRUE)

  • annotation.arrowcolor - Annotation arrow color (UI: "Arrow Color", default: "black")

  • annotation.arrowhead - Annotation arrowhead style (UI: "Arrowhead Style", default: 2)

  • annotation.arrowwidth - Annotation arrow line width (UI: "Arrow Linewidth", default: 1.5)

See also

dittoViz::yPlot(), organize_inputs(), dittoViz_yPlotOutputUI(), dittoViz_yPlotServer(), dittoViz_yPlotApp()

Author

Jared Andrews, Jacob Martin

Examples

if (FALSE) { # interactive()
library(VizModules)
data(mtcars)
dittoViz_yPlotInputsUI("yPlot", mtcars)
}