procNiceOptions: Process plotting options

In ZachHunter/NicePlots.R: Nice Plots for Data Exploration

Process plotting options

Description

Integrates theme and user arguments to finalize all options prior to plotting

Usage

procNiceOptions(
  x,
  by,
  minorTick,
  pointShape,
  whiskerLineType,
  lWidth,
  capWidth,
  pointLaneWidth,
  width,
  guides,
  pointSize,
  subgroup = FALSE,
  stack = F,
  pointHighlights = F,
  type = c("BP", "VP", "DP", "Bar"),
  theme,
  plotColors,
  pointMethod,
  logScale,
  drawPoints,
  groupLabels,
  subgroupLabels = NULL,
  highlightLabels = NULL,
  swarmOverflow,
  errorCap = NULL,
  CLOptions = NULL
)

Arguments

x	Data to be plotted which has been pre-processed by dataFlightCheck
by	factor or data.frame of factors; One or more factors that control how the data is grouped. The first column is the primary grouping factor and the second and thrid columns are used for sub-grouping and highlighting as needed.
minorTick	numeric; Number of minor tick marks to be drawn between the major marks
pointShape	numeric; vector of numbers corresponding to pty options for ploting data overlays.
whiskerLineType	numeric; number corresponding to lty option for drawing the whiskers and error bars for box plots and bar plots, respectively.
lWidth	numeric; number corresponding to the lwd option for plotting lines on the graph
capWidth	numeric; Width of the cap relative to the bar/box width for box plots and bar plots.
pointLaneWidth	numeric; This controls how far data point dots can move along the categorical axis when plotting. Used for pointMethod options 'jitter', 'beeswarm', and 'distribution'.
width	numeric; A multiplier that controls how wide the plotting elements will be. Setting width=1.1 would result in plot elements being 10% wider.
guides	logical; Should guidelines be drawn at the major tick marks.
pointSize	numeric; A numeric vector controlling the size of points on the data overlay
subgroup	logical; Should the data be faceted into subgroups within the primary factor levels. Ignored if by is a factor.
stack	logical; Triggers stacked bar analysis for bar plots
pointHighlights	logical; will use additional factors in by to highlight points in the dot plot
type	character; What kind of plot is this for? Case sensitive options are "BP", "DP", "VP", and "Bar" corresponding to box plots, dot plots, violin plots, and bar plots, respectively.
theme	list object; Themes are are an optional way of storing graphical preset options that are compatible with all nicePlot graphing functions.
plotColors	list; a named list of vectors of colors that set the color options for all NicePlot functions. Names left unspecified will be added and set to default values automatically.
pointMethod	character; method to be used for ploting dots. Can be set to "jitter", "linear", "beeswarm" or "distribution".
logScale	numeric; Should a log scale use used (TRUE/FALSE)? Otherwise indicates the base for the log transformation.
drawPoints	logical; draws a dot plot overlay of the data.
groupLabels	character; A character vector to override factor labels for primary group names
subgroupLabels	character; A character vector to override factor labels for subgroup names
highlightLabels	character; A character vector to override factor labels for point highlights.
swarmOverflow	character; Valid options are: "none", "wrap", "gutter", "random", and "omit". Controls how to wantly point stacks that would overflow the pointLaneWidth option.
errorCap	character; Determines the style for the ends of the error bars. Valid options are ball, bar or none.
CLOptions	list; A list of command line options captured by ... being passed along to allow for theme values to be set directly from the function call even if it is not an explicit option.

Details

This is a private utility function used by NicePlots to integrate user options with theme defaults. Anything specified by the user is treated literally with no additional optimization. Colors, point shapes, fills, etc. are optimized to best enhance the relevant factor visualizations selected. The finalized parameters are returned as a named list.

Value

Named listed of graphical options

See Also

formatPlotColors, niceBox, niceDots, niceVio, niceBar

ZachHunter/NicePlots.R documentation built on Sept. 23, 2023, 4:04 a.m.