gplots (version 3.2.0)

plotCI: Plot Error Bars and Confidence Intervals

Description

Given a set of x and y values and interval width or upper and lower bounds, plot the points with error bars. This can be a useful tool for visualizing confidence intervals.

Usage

plotCI(x, y = NULL, uiw, liw = uiw, ui, li, err='y', ylim=NULL,
       xlim=NULL, type="p",  col=par("col"), barcol=col,
       pt.bg = par("bg"),  sfrac = 0.01, gap=1, lwd=par("lwd"),
       lty=par("lty"), labels=FALSE, add=FALSE, xlab, ylab,  minbar,
       maxbar, ... )

Arguments

x,y

coordinates for the center of error bars. y defaults to 1:n.

uiw

width of the upper or right error bar. Set to NULL or NA to omit upper bars.

liw

width of the lower or left error bar. Defaults to same value as uiw. Set to NULL or NA to omit lower bars.

ui

upper end of error bars. Defaults to y + uiw or x + uiw depeding on err. Set to NULL or NA to omit upper bars.

li

lower end of error bars. Defaults to y - liw or x - liw depedning on err. Set to NULL or NA to omit lower bars.

err

direction for error bars. Set to "y" for vertical bars. Set to "x" for horizontal bars. Defaults to "y".

col

color of plotting character used center marker of error bars. Default is "black".

xlim, ylim

range of x/y values to include in the plotting area.

type

point/line type; passed to points

barcol

color of the error bars. Defaults to the same value as col

pt.bg

background color of points (use pch=21, pt.bg=par("bg") to get open points superimposed on error bars).

sfrac

width of "crossbar" at the end of error bar as a fraction of the x plotting region. Defaults to 0.01.

gap

space left between the center of the error bar and the lines marking the error bar in units of the height (width) of the letter "O". Defaults to 1.0

lwd

width of bar lines.

lty

line type of bar lines.

labels

either a logical value indicating whether the circles representing the x values should be replaced with text giving the actual values or a vector containing labels to use instead. Defaults to FALSE.

add

logical indicating whether error bars should be added to the current plot. If FALSE (the defailt), a new plot will be created and symbols/labels for the x values will be plotted before drawing error bars.

minbar

minumum allowed value for bar ends. If specified, values smaller than minbar will be replaced with minbar.

maxbar

maximum allowed value for bar ends. If specified, values larger than maxbar will be replaced with maxbar.

...

optional plotting parameters

xlab

label for x axis.

ylab

label for y axis.

Author

Original version by Bill Venables posted to r-help on Sep. 20, 1997. Enhanced version posted to r-help by Ben Bolker on Apr. 16, 2001. This version was modified and extended by Gregory R. Warnes . Additional changes suggested by Martin Maechler integrated on July 29, 2004.

See Also

plotmeans provides an enhanced wrapper to plotCI.

Examples

  # plot means and
  data(state)
  tmp   <- split(state.area, state.region)
  means <- sapply(tmp, mean)
  stdev <- sqrt(sapply(tmp, var))
  n     <- sapply(tmp,length)
  ciw   <- qt(0.975, n) * stdev / sqrt(n)

  # plain
  plotCI(x=means, uiw=ciw)

  # prettier
  plotCI(x=means, uiw=ciw, col="black", barcol="blue", lwd=1)

  # give mean values
  plotCI(x=means, uiw=ciw, col="black", barcol="blue",
         labels=round(means,-3), xaxt="n", xlim=c(0,5) )
  axis(side=1, at=1:4, labels=names(tmp), cex=0.7)

  # better yet, just use plotmeans ... #
  plotmeans( state.area ~ state.region )

# \dontshow{
## Just for testing
  plotCI(x=means, uiw=NA)
  plotCI(x=means, uiw=NULL)
  plotCI(x=means, uiw=ciw)
  plotCI(x=means, uiw=ciw, liw=NULL)
  plotCI(x=means, uiw=ciw, liw=NA)
  plotCI(x=means, liw=ciw, ciw=NULL)
  plotCI(x=means, liw=ciw, ciw=NA)
  ciw.na <- ciw
  ciw.na[3] <- NA
  plotCI(x=means, uiw=ciw.na, liw=ciw)
  plotCI(x=means, liw=ciw.na, uiw=ciw)
# }