DescTools: PlotDot – R documentation

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PlotDot

Cleveland's Dot Plots

Description

Draw a Cleveland dot plot. This is an extended version of dotchart with an added option for error bars and an add argument.

Usage

PlotDot(x, labels = NULL, groups = NULL, gdata = NULL,
        cex = par("cex"), pch = 21, gpch = 21, bg = par("bg"),
        color = par("fg"), gcolor = par("fg"), lcolor = "gray", lblcolor = par("fg"),
        xlim = NULL, main = NULL, xlab = NULL, ylab = NULL,
        xaxt=NULL, yaxt=NULL, add = FALSE, args.errbars = NULL, 
        cex.axis = par("cex.axis"), cex.pch = 1.2, cex.gpch=1.2, ...)

Arguments

`x`	either a vector or matrix of numeric values (`NA`s are allowed). If `x` is a matrix the overall plot consists of juxtaposed dotplots for each row. Inputs which satisfy `is.numeric(x)` but not `is.vector(x) \|\| is.matrix(x)` are coerced by `as.numeric`, with a warning.
`labels`	a vector of labels for each point. For vectors the default is to use `names(x)` and for matrices the row labels `dimnames(x)[[1]]`.
`groups`	an optional factor indicating how the elements of `x` are grouped. If `x` is a matrix, `groups` will default to the columns of `x`.
`gdata`	data values for the groups. This is typically a summary such as the median or mean of each group.
`cex`	the character size to be used. Setting `cex` to a value smaller than one can be a useful way of avoiding label overlap. Unlike many other graphics functions, this sets the actual size, not a multiple of `par("cex")`.
`pch`	the plotting character or symbol to be used. Default is 21.
`gpch`	the plotting character or symbol to be used for group values.
`bg`	the background color of plotting characters or symbols to be used; use `par(bg= *)` to set the background color of the whole plot.
`color`	the color(s) to be used for points and labels.
`gcolor`	the single color to be used for group labels and values.
`lcolor`	the color(s) to be used for the horizontal lines.
`lblcolor`	the color(s) to be used for labels.
`xlim`	horizontal range for the plot, see `plot.window`, e.g.
`main`	overall title for the plot, see `title`.
`xlab, ylab`	axis annotations as in `title`.
`xaxt`	a character which specifies the x axis type. Specifying `"n"` suppresses plotting of the axis.
`yaxt`	a character which specifies the y axis type. Specifying `"n"` suppresses plotting of the axis.
`add`	logical specifying if bars should be added to an already existing plot; defaults to `FALSE`.
`args.errbars`	optional arguments for adding error bars. All arguments for `ErrBars` can be supplied. If left to `NULL` (default), no error bars will be plotted.
`cex.axis`	The magnification to be used for axis annotation relative to the current setting of cex.
`cex.pch`	The magnification to be used for plot symbols relative to the current setting of cex.
`cex.gpch`	The magnification to be used for group symbols relative to the current setting of cex.
`...`	graphical parameters can also be specified as arguments.

Details

This function is invoked for its side effect, which is to produce two variants of dotplots as described in Cleveland (1985).

Dot plots are a reasonable substitute for bar plots.

Value

Return the y-values used for plotting.

Author(s)

R-Core with some extensions by Andri Signorell <andri@signorell.net>

References

Becker, R. A., Chambers, J. M. and Wilks, A. R. (1988) The New S Language. Wadsworth & Brooks/Cole.

Cleveland, W. S. (1985) The Elements of Graphing Data. Monterey, CA: Wadsworth.

Murrell, P. (2005) R Graphics. Chapman & Hall/CRC Press.

Examples

PlotDot(VADeaths, main = "Death Rates in Virginia - 1940")
op <- par(xaxs = "i")  # 0 -- 100%
PlotDot(t(VADeaths), xlim = c(0,100),
        main = "Death Rates in Virginia - 1940")
par(op)

# add some error bars
PlotDot(VADeaths, main="Death Rates in Virginia - 1940", col="red", pch=21,
        args.errbars = list(from=VADeaths-2, to=VADeaths+2, mid=VADeaths,
                            cex=1.4))

# add some other values
PlotDot(VADeaths+3, pch=15, col="blue", add=TRUE, labels=NA)

# same as PlotDotCI
xci <- do.call(rbind, tapply( d.pizza$delivery_min, d.pizza$driver,
                              MeanCI, conf.level=0.99, na.rm=TRUE))

PlotDot(xci[,1], main="delivery_min ~ driver", pch=21, bg="grey80", col="black",
        args.errbars = list(from=xci[,2], to=xci[,3], mid=xci[,1], lwd=2, col="grey40", cex=1.5),
        xlim=c(15,35), panel.before=grid())

# with group data
x <- with(d.pizza, tapply(temperature, list(area, driver), mean, na.rm=TRUE))

PlotDot(x, gdata = tapply(d.pizza$temperature, d.pizza$driver, mean, na.rm=TRUE),
        gpch = 15)

# special format
par(lend=1)

PlotDot(VADeaths, main="Death Rates in Virginia - 1940", pch="|", lcolor = hecru, col=hred,
        args.errbars = list(from=VADeaths-2, to=VADeaths+2, mid=VADeaths,
                            cex=1.3, lwd=8, code=0, col=hgreen))

# Error bars for binomial confidence intervals
tab <- table(d.pizza$driver, d.pizza$wine_delivered)
xci <- SetNames(BinomCI(tab[,1], rowSums(tab)), rownames=rownames(tab))
PlotDot(xci[,1], main="wine delivered ~ driver ", xlim=c(0,1),
        args.errbars=list(from=xci[,-1], mid=xci[,1], pch=21))


# Error bars for confidence intervals for means
xci <- do.call(rbind, tapply(d.pizza$delivery_min, d.pizza$driver,
                             MeanCI, conf.level=0.99, na.rm=TRUE))

PlotDot(xci[, 1], main="delivery_min ~ driver", args.errbars=list(from=xci))


# Setting the colours
# define some error bars first
lci <- sweep(x = VADeaths, MARGIN = 2, FUN = "-", 1:4)
uci <- sweep(x = VADeaths, MARGIN = 1, FUN = "+", 1:5)

PlotDot(VADeaths, main="This should only show how to set the colours, not be pretty",
        pch=21, col=c("blue","grey"), bg=c("red", "yellow"),
        gcolor = c("green", "blue", "orange", "magenta"), gdata=c(10,20,30,40),
        gpch = c(15:18), lcolor = "orange",
        args.errbars = list(from=lci, to=uci, mid=VADeaths, cex=1.4))

DescTools

Tools for Descriptive Statistics

v0.99.41

GPL (>= 2)

Authors

Andri Signorell [aut, cre], Ken Aho [ctb], Andreas Alfons [ctb], Nanina Anderegg [ctb], Tomas Aragon [ctb], Chandima Arachchige [ctb], Antti Arppe [ctb], Adrian Baddeley [ctb], Kamil Barton [ctb], Ben Bolker [ctb], Hans W. Borchers [ctb], Frederico Caeiro [ctb], Stephane Champely [ctb], Daniel Chessel [ctb], Leanne Chhay [ctb], Nicholas Cooper [ctb], Clint Cummins [ctb], Michael Dewey [ctb], Harold C. Doran [ctb], Stephane Dray [ctb], Charles Dupont [ctb], Dirk Eddelbuettel [ctb], Claus Ekstrom [ctb], Martin Elff [ctb], Jeff Enos [ctb], Richard W. Farebrother [ctb], John Fox [ctb], Romain Francois [ctb], Michael Friendly [ctb], Tal Galili [ctb], Matthias Gamer [ctb], Joseph L. Gastwirth [ctb], Vilmantas Gegzna [ctb], Yulia R. Gel [ctb], Sereina Graber [ctb], Juergen Gross [ctb], Gabor Grothendieck [ctb], Frank E. Harrell Jr [ctb], Richard Heiberger [ctb], Michael Hoehle [ctb], Christian W. Hoffmann [ctb], Soeren Hojsgaard [ctb], Torsten Hothorn [ctb], Markus Huerzeler [ctb], Wallace W. Hui [ctb], Pete Hurd [ctb], Rob J. Hyndman [ctb], Christopher Jackson [ctb], Matthias Kohl [ctb], Mikko Korpela [ctb], Max Kuhn [ctb], Detlew Labes [ctb], Friederich Leisch [ctb], Jim Lemon [ctb], Dong Li [ctb], Martin Maechler [ctb], Arni Magnusson [ctb], Ben Mainwaring [ctb], Daniel Malter [ctb], George Marsaglia [ctb], John Marsaglia [ctb], Alina Matei [ctb], David Meyer [ctb], Weiwen Miao [ctb], Giovanni Millo [ctb], Yongyi Min [ctb], David Mitchell [ctb], Franziska Mueller [ctb], Markus Naepflin [ctb], Daniel Navarro [ctb], Henric Nilsson [ctb], Klaus Nordhausen [ctb], Derek Ogle [ctb], Hong Ooi [ctb], Nick Parsons [ctb], Sandrine Pavoine [ctb], Tony Plate [ctb], Luke Prendergast [ctb], Roland Rapold [ctb], William Revelle [ctb], Tyler Rinker [ctb], Brian D. Ripley [ctb], Caroline Rodriguez [ctb], Nathan Russell [ctb], Nick Sabbe [ctb], Ralph Scherer [ctb], Venkatraman E. Seshan [ctb], Michael Smithson [ctb], Greg Snow [ctb], Karline Soetaert [ctb], Werner A. Stahel [ctb], Alec Stephenson [ctb], Mark Stevenson [ctb], Ralf Stubner [ctb], Matthias Templ [ctb], Duncan Temple Lang [ctb], Terry Therneau [ctb], Yves Tille [ctb], Luis Torgo [ctb], Adrian Trapletti [ctb], Joshua Ulrich [ctb], Kevin Ushey [ctb], Jeremy VanDerWal [ctb], Bill Venables [ctb], John Verzani [ctb], Pablo J. Villacorta Iglesias [ctb], Gregory R. Warnes [ctb], Stefan Wellek [ctb], Hadley Wickham [ctb], Rand R. Wilcox [ctb], Peter Wolf [ctb], Daniel Wollschlaeger [ctb], Joseph Wood [ctb], Ying Wu [ctb], Thomas Yee [ctb], Achim Zeileis [ctb]

Initial release

2021-04-09