vioplotW: Violin-Plots Version W

Description

This function allows generating Violin plots) using a variety of input formats and offers additional options for colors. Main input may be multiple vectors, a matrix or list of multiple data-elements (entries may be of variable length), individual colors for different sets of data or color-gradients can be specified, and the display of n per set of data was integtated (based on an inspiration from the discussion 'Removing-NAs-from-dataframe-for-use-in-Vioplot' on the forum Nabble). It is also possible to plot pairwise half-violins for easier pairwise-comparisons (using halfViolin="pairwise"). Many arguments are kept similar to vioplot (here, the package vioplot is not required/used).

Usage

vioplotW(
  x,
  ...,
  finiteOnly = TRUE,
  removeEmpty = FALSE,
  halfViolin = FALSE,
  boxCol = "def",
  hh = NULL,
  xlim = NULL,
  ylim = NULL,
  nameSer = NULL,
  cexNameSer = NULL,
  horizontal = FALSE,
  col = "rainbow",
  border = "black",
  xlab = NULL,
  ylab = NULL,
  cexLab = NULL,
  cexAxis = NULL,
  lty = 1,
  pointCol = NULL,
  cexPt = NULL,
  tit = NULL,
  las = 1,
  lwd = 1,
  rectCol = "black",
  at = 0,
  add = FALSE,
  wex = NULL,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Value

This function plots a figure (to the current graphical device)

Arguments

x: (matrix, list or data.frame) data to plot, or first series of data
...: (numeric) additional sets of data to plot
finiteOnly: (logical) eliminate non-finite elements to avoid potential errors (eg when encountering NA)
removeEmpty: (logical) omit empty series (or less than 4 finite numeric entries) of data from plot
halfViolin: (logical or character) decide with TRUE or FALSE if full or only half of violins should be plotted, if "pairwise" always 2 data-sets will be plotted back-to-back
boxCol: (character) decide if boxplot should be adde inside the violin, use "def" for default transparent grey
hh: (numeric, length <4) smoothing parameter (standard deviation to kernel function, if omited anormal optimal smoothing parameter is used); equivalent to argument h in package vioplot ; see also sm.density
xlim: (NULL or numeric, length=2) custom limit on x-axis, see also par
ylim: (NULL or numeric, length=2) custom limit on y-axis, see also par
nameSer: (character) custom label for data-sets or columns (length must match number of data-sets)
cexNameSer: (numeric) size of individual data-series labels as cex-expansion factor (see also par)
horizontal: (logical) orientation of plot
col: (character or integer) custom colors or gradients like 'rainbow', 'grayscale', 'heat.colors', 'topo.colors', 'Spectral' or 'Paired', or you may use colors made by the package colorRamps
border: (character) custom color for figure border
xlab: (character) custom x-axis label
ylab: (character) custom y-axis label
cexLab: (numeric) size of axis labels as cex-expansion factor (see also par)
cexAxis: (numeric) size of numeric y-axis labels as cex-expansion factor (see also par)
lty: (integer) line-type for linear regression line (see also par)
pointCol: (character or numeric) display of median: color (defauly white)
cexPt: (numeric) display of median : size of point as cex-expansion factor (see also par)
tit: (character) custom title to figure
las: (integer) orientation of axis labels (see also par)
lwd: (integer) width of line(s) (see also par)
rectCol: (character) color of rectangle
at: (numeric) custom locoation of data-series names, ie the points at which tick-marks are to be drawn, will be passed to axis, it's length ust match the number of data-sets
add: (logical) add to existing plot if TRUE
wex: (integer) relative expansion factor of the violin
silent: (logical) suppress messages
debug: (logical) additional messages for debugging
callFrom: (character) allow easier tracking of messages produced

Details

The (relative) width of the density-profiles ('Violins') may be manually adjusted using the parameter wex which applies to all profiles drawn.

Note : Arguments have to be given with full names, lazy evaluation of arguments will not work properly with this function (since '...' is used to capture additional data-sets). Note : vioplot offers better options for plotting formulas

Examples

Run this code

set.seed(2013)
dat6 <- matrix(round(rnorm(300) +3, 1), ncol=6,
	 dimnames=list(paste0("li",1:50), letters[19:24]))
vioplotW(dat6)
## variable number of elements (each n is displayed)
dat6b <- apply(dat6, 2, function(x) x[which(x < 5)])
dat6b[[4]] <- dat6b[[4]][dat6b[[4]] < 4]
vioplotW(dat6b, col="Spectral")
vioplotW(dat6b, col="Spectral" ,halfViolin="pairwise", horizontal=TRUE)
vioplotW(dat6b, col="Spectral", halfViolin="pairwise", horizontal=FALSE)