histW: Histogram (version by WR)

In wrGraph: Graphics in the Context of Analyzing High-Throughput Data

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 messages for debugging
callFrom	(character) allow easier tracking of messages produced

Value

This function produces a histogram type graphic (to the ccurrent graphical device)

See Also

hist

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 documentation built on Oct. 20, 2023, 5:08 p.m.