1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
|
\name{centipede.plot}
\alias{centipede.plot}
\title{Display a centipede plot}
\description{
Displays a centipede plot on the current graphics device.
}
\usage{
centipede.plot(segs,mct="mean",lower.limit="std.error",
upper.limit=lower.limit,left.labels=NULL,right.labels=NULL,sort.segs=TRUE,
main="",xlab=NA,pch=21,vgrid=NA,hgrid=NA,gridcol="lightgray",mar=NA,col=par("fg"),
bg="green",...)
}
\arguments{
\item{segs}{a matrix of midpoints and limits calculated by
\link{get.segs} OR a \samp{dstat} object returned by
\samp{brkdn}.}
\item{mct}{The function to use in calculating the midpoint of each
segment.}
\item{lower.limit}{The functions to use in calculating the
lower limits for each subset of the data.}
\item{upper.limit}{The functions to use in calculating the
upper limits.}
\item{left.labels}{The variable or subset labels to place at the left margin of
the plot. Default values are provided.}
\item{right.labels}{The variable or subset labels to place at the right margin
of the plot.}
\item{sort.segs}{Whether to sort the segments in ascending order.}
\item{main}{Optional title for the plot.}
\item{xlab}{Optional x axis label for the plot. The default NA
displays a text label showing the midpoint and limit functions.}
\item{pch}{The symbols to use when plotting midpoints.}
\item{vgrid}{Optional vertical line(s) to display on the plot. Defaults to
NA (none).}
\item{hgrid}{Optional horizontal grid lines to display on the plot. Defaults
to NA (none).}
\item{gridcol}{The color for the vgrid and hgrid lines.}
\item{mar}{Margin widths for the plot. Defaults to c(4,5,1,4) or
c(4,5,3,4) if there is a title.}
\item{col}{The color(s) of the limit lines and borders of the midpoint
markers.}
\item{bg}{The color(s) to fill the midpoint markers.}
\item{...}{additional arguments passed to \samp{plot}.}
}
\details{
\samp{centipede.plot} displays one or more midpoints and limits as
filled circles with horizontal error bars. It places labels on the left and
right sides of the plot. If these labels are long, it may be necessary to
pass explicit values to the \samp{mar} argument to leave enough room.
The \samp{vgrid} argument is usually used to display an average value for
all of the midpoints. If one or more values are passed in this argument,
they will be displayed as vertical lines spanning the plot. The \samp{hgrid}
argument acts like the \samp{grid} function, drawing dashed horizontal lines
across the plot. If \samp{hgrid=NULL}, these lines will be drawn under the
values displayed, which will be 1 to the number of values on the vertical axis.
The user can pass explicit values if desired. With horizontal and optionally
vertical grid lines, the centipede plot is practically equivalent to a dotplot
with error bars.
Similarly, centipede plots typically have a large number of subsets, and
it may be necessary to start the graphics device with an aspect ratio that
will prevent crowding of the labels when over 30 segments are displayed.
The matrix \samp{segs} may be entered manually or read from a file.
The first row specifies midpoints, the second and third rows the lower
and upper limits respectively and the fourth row the number of valid
observations. If there are no values for number of valid observations,
just pass vector of blank strings with the \samp{right.labels} argument.
If a \samp{dstat} object is passed as \samp{segs}, the function will calculate
the lower and upper values according to the relevant arguments. This type of
plot is also known as a caterpillar plot or a league table.
}
\value{nil.}
\author{Jim Lemon}
\seealso{\link{get.segs}}
\examples{
testcp<-list("",40)
for(i in 1:40) testcp[[i]]<-rnorm(sample(1:8,1)*50)
segs<-get.segs(testcp)
centipede.plot(segs,main="Test centipede plot",vgrid=0)
# now leave out the number of valid observations, pass x labels and no right labels
centipede.plot(segs[1:3,],main="Test centipede plot",vgrid=0,mar=c(4,5,3,2),
left.labels=paste("X",1:40,sep=""),right.labels=rep("",40))
}
\keyword{misc}
|
