gplots (version 3.2.0)

plotmeans: Plot Group Means and Confidence Intervals

Description

Plot group means and confidence intervals.

Usage

plotmeans(formula, data=NULL, subset, na.action,
          bars=TRUE, p=0.95, minsd=0, minbar, maxbar,
          xlab=names(mf)[2], ylab=names(mf)[1], mean.labels=FALSE,
          ci.label=FALSE, n.label=TRUE, text.n.label="n=",
          digits=getOption("digits"), col="black", barwidth=1,
          barcol="blue", connect=TRUE, ccol=
          col, legends=names(means), xaxt, use.t=TRUE,
          lwd=par("lwd"), ...)

Arguments

formula

symbolic expression specifying the outcome (continuous) and grouping variable (factor). See lm() for details.

data

optional data frame containing the variables in the model.

subset

an optional vector specifying a subset of observations to be used in the fitting process.

na.action

a function which indicates what should happen when the data contain `NA's. See lm() for details.

bars

a logical value indicating whether confidence interval bars should be plotted. Defaults to TRUE.

p

confidence level for error bars. Defaults to 0.95.

minsd

minumum permitted value for the standard deviation within each factor level. Any standard deviation estimates smaller than minsd will be replaced with minsd. Defaults to 0.

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.

xlab

x-axis label.

ylab

y-axis label.

mean.labels

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

ci.label

a logical value indicating whether text giving the actual interval end values should be placed at the end of each confidence interval bar. Defaults to FALSE.

n.label

a logical value indicating whether text giving the number of observations in each group should should be added to the plot.

text.n.label

Prefix text for labeling observation counts. Defaults to "n=".

digits

number of significant digits to use when displaying mean or confidince limit values.

col

color of cicles marking group means. Default is "black".

barwidth

linewidth of interval bars and end marks. Default is 1.

barcol

color of interval bars and end marks. Default is "blue".

connect

either a logical value indicating whether the means of each group should be connected by a line, or a list of vectors giving the index of bars that should be connected by a line. Defaults to TRUE.

ccol

color of lines used to connect means. Defaults to the same color as "col".

legends

vector containing strings used to label groups along the x axis. Defaults to group names.

xaxt

A character which specifies the axis type. Specifying `"n"' causes an axis to be set up, but not plotted.

use.t

a logical value indicating whether the t distribution should be used to compute confidence intervals. If TRUE, the default, a t distribution will the correct number of degrees of freedom for each group be used. If FALSE, the a normal distribution will be used.

lwd

Width of connecting lines

...

optional plotting parameters.

Author

Gregory R. Warnes

See Also

plotCI, boxplot

Examples

  # library(gplots)
  # show comparison with boxplot
  data(state)
  plotmeans(state.area ~ state.region)

  # show some color and mean labels
  plotmeans(state.area ~ state.region,
             mean.labels=TRUE, digits=-3,
             col="red", connect=FALSE)

  # show how to specify which means should be connected
  plotmeans(state.area ~ state.region, connect=list(1:2, 3:4),
            ccol="red", pch=7 )

  # more complicated example showing how to show an interaction
  data(esoph)
  par(las=2,                        # use perpendicular axis labels
      mar=c(10.1,4.1,4.1,2.1),      # create enough space for long x labels
      mgp=c(8,1,0)                  # move x axis legend down to avoid overlap
      )
  plotmeans(ncases/ncontrols ~ interaction(agegp , alcgp, sep ="   "),
            connect=list(1:6,7:12,13:18,19:24),
            barwidth=2,
            col="dark green",
            data=esoph,
            xlab="Age Group and Alcohol Consumption",
            ylab="# Cases / # Controls",
            ylim = c(-.9,1.4),
            main=c("Fraction of Cases for by Age and Alcohol Consumption",
                   "Ile-et-Vilaine Esophageal Cancer Study")
            )
  abline(v=c(6.5, 12.5, 18.5), lty=2)