wrGraph: vioplotW – R documentation

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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 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). 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

Usage

vioplotW(
  x,
  ...,
  finiteOnly = TRUE,
  halfViolin = FALSE,
  boxCol = "def",
  hh = NULL,
  ylim = NULL,
  nameSer = NULL,
  cexNameSer = NULL,
  horizontal = FALSE,
  col = "rainbow",
  border = "black",
  xlab = 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
)

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`)
`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`
`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 axis label
`cexLab`	(numeric) size of axis labels as cex-expansion factor (see also `par`)
`cexAxis`	(numeric) size of numerix 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 message(s) produced

Details

The (relative) width of the density-profiles ('Violins') may be manually adjusted using the parameter wex which applieds to all profiles drawn. Please note that different n (eg for different columns) will not be shown, so far.

Value

figure only

Examples

set.seed(2013)
dat6 <- matrix(round(rnorm(300) +3, 1), ncol=6, 
	 dimnames=list(paste("li",1:50,sep=""), 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)

wrGraph

Graphics in the Context of Analyzing High-Throughput Data

v1.2.3

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release