wrGraph: histW – R documentation

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histW

Histogram (version by WR)

Description

This function proposes a few special tweaks to the general hist function : In a number of settings data are treated and plotted as log-data. This function allows feeding directly log2-data and displaying the x-axis (re-translated) in linear scale (see argument isLog). The default settings allow making (very) small histograms ('low resolution'), which may be used as a rough overview of bandwidth and distribution of values in dat. Similar to hist, by changing the parameters nBars and/or breaks very 'high resolution' histograms can be produced. By default it displays n per set of data (on the top of the figure). Note that the argument for (costom) title main is now called tit.

Usage

histW(
  dat,
  fileName = "histW",
  output = "screen",
  nBars = 8,
  breaks = NULL,
  tit = NULL,
  subTi = NULL,
  xLab = NULL,
  yLab = NULL,
  las = NULL,
  xcex = 0.7,
  imgxSize = 900,
  useCol = NULL,
  useBord = NULL,
  isLog = TRUE,
  cexSubTi = NULL,
  cropHist = TRUE,
  parDefault = TRUE,
  silent = FALSE,
  debug = FALSE,
  callFrom = NULL
)

Arguments

`dat`	(matrix, list or data.frame) data to plot
`fileName`	(character) name of file for saving graphics
`output`	(character, length=1) options for output on 'screen' or saving image in various formats (set to 'jpg','png' or 'tif')
`nBars`	(integer) number of bars in histogram (default for 'low resolution' plot to give rough overview)
`breaks`	(integer) for (partial) compatibility with hist() : use only for number of breaks (or 'FD'), gets priority over 'nBars'
`tit`	(character) custom title
`subTi`	(character) may be `FALSE` for NOT displaying, or any text, otherwise range
`xLab`	(character) custom x-axes label
`yLab`	(character) custom y-axes label
`las`	(integer) optional fixed text orientation of x-axis numbers : use 1 for horizontal and 2 for perpendicular, see also `par`
`xcex`	(numeric) cex-type expansion factor for x-axis numbers, see also `par`
`imgxSize`	(integer) width of image when saving to file, see also `par`
`useCol`	(character or integer) custom colors, see also `par`
`useBord`	(character) custom histogram elements border color, see also `par`
`isLog`	(logical) for lin scale signal intensity values where repesentation needs log, assume log2 if `TRUE`
`cexSubTi`	(numerical) subtitle size (expansion factor cex), see also `par`
`cropHist`	(logical) -not implemented yet- designed for cutting off bars with very low ('insignificant') values
`parDefault`	(logical) to automatic adjusting par(marg=,cex.axis=0.8), see also `par`
`silent`	(logical) suppress messages
`debug`	(logical) additonal messagesfor debugging
`callFrom`	(character) allow easier tracking of message(s) produced

Examples

set.seed(2016); dat1 <- round(c(rnorm(200,6,0.5),rlnorm(300,2,0.5),rnorm(100,17)),2)
dat1 <- dat1[which(dat1 <50 & dat1 > 0.2)]
histW(dat1,br="FD",isLog=FALSE)
histW(log2(dat1),br="FD",isLog=TRUE)

## quick overview of distributions  
layout(partitionPlot(4))
for(i in 1:4) histW(iris[,i],isLog=FALSE,tit=colnames(iris)[i])

wrGraph

Graphics in the Context of Analyzing High-Throughput Data

v1.2.3

GPL-3

Authors

Wolfgang Raffelsberger [aut, cre]

Initial release