gplots: ooplot – R documentation

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ooplot

Create an OpenOffice style plot

Description

An extension of barplot2. Creates bar- and line-plots mimicking the style of OpenOffice plots. This utility can plot the values next to each point or bar as well as confidence intervals.

Usage

ooplot(data, ...)
## Default S3 method:
ooplot(data, width=1, space=NULL, names.arg=NULL, 
                           legend.text=NULL, horiz=FALSE, 
                           density=NULL, angle=45, kmg="fpnumkMGTP", 
                           kmglim=TRUE, 
                           type=c("xyplot", "linear", "barplot", "stackbar"), 
                           col=heat.colors(NC), prcol=NULL, 
                           border=par("fg"), main=NULL, sub=NULL, 
                           xlab=NULL, ylab=NULL, xlim=NULL, ylim=NULL, 
                           xpd=TRUE, log="", axes=TRUE, 
                           axisnames=TRUE, prval=TRUE, lm=FALSE,
                           cex.axis=par("cex.axis"), 
                           cex.names=par("cex.axis"),
                           cex.values=par("cex"),inside=TRUE, 
                           plot=TRUE, axis.lty=0, plot.ci=FALSE, 
                           ci.l=NULL, ci.u=NULL, ci.color="black", 
                           ci.lty="solid", ci.lwd=1, plot.grid=FALSE, 
                           grid.inc=NULL, grid.lty="dotted", 
                           grid.lwd=1, grid.col="black", add=FALSE, 
                           by.row=FALSE, ...)

Arguments

`data`	a matrix of values describing the values that make up the plot. The first column of `data` is taken as the axis against which all the other values are plotted. The first column of `data` may not be sparse.
`width`	optional vector of barwidths. Re-cycled to the number of bars drawn. A single value will have no visible effect.
`space`	the amount of space left before each bar. May be given as a single number or one number per bar. If `type` is `stackbar`, `space` may be specified by two numbers, where the first is the space between bars in the same group, and the second the space between groups. Defaults to `c(0,1)` if `type` is a `stackbar`, and to 0.2 otherwise.
`names.arg`	a vector of names to be plotted below each bar or group of bars. If this argument is omitted, then the names are taken from the row names of `data`.
`legend.text`	a vector of text used to construct a legend for the plot, or a logical indicating whether a legend should be included; if `legend.text` is true, the row names of `data` will be used as labels if they are non-null.
`horiz`	a logical value. If `FALSE`, the bars are drawn vertically with the first bar to the left. If `TRUE`, the bars are drawn horizontally with the first at the bottom.
`density`	a vector giving the the density of shading lines, in lines per inch, for the bars or bar components. The default value of `NULL` means that no shading lines are drawn. Non-positive values of `density` also inhibit the drawing of shading lines.
`angle`	the slope of shading lines, given as an angle in degrees (counter-clockwise), for the bars or bar components.
`kmg`	the set of SI units to convert, defaults to "fpnumkMGTP". See below for details.
`kmglim`	logical. If `FALSE` the conversion to SI units is not performed. Default is `TRUE`.
`type`	a string indicating the preferred format of the plot, choices are: xyplot : plot where y is plotted against the x-value. linear : plot where y values are plotted against equidistant x-values. barplot : plot where y values are represented as bars against equidistant x-values. stackplot : plot where y values are stacked for identical x-values and bars are equidistant.
`col`	a vector of colors for the bars or bar components.
`prcol`	the color to be used for the plot region.
`border`	the color to be used for the border of the bars.
`main, sub`	overall and sub titles for the plot.
`xlab`	a label for the x axis.
`ylab`	a label for the y axis.
`xlim`	limits for the x axis.
`ylim`	limits for the y axis.
`xpd`	logical. Should bars be allowed to go outside region?
`log`	a character string which contains ‘"x"’ if the x axis is to be logarithmic, ‘"y"’ if the y axis is to be logarithmic and ‘"xy"’ or ‘"yx"’ if both axes are to be logarithmic.
`axes`	logical. If `TRUE`, a vertical (or horizontal, if `horiz` is true) axis is drawn.
`axisnames`	logical. If `TRUE`, and if there are `names.arg` (see above), the other axis is drawn (with `lty=0`) and labeled.
`prval`	logical. If `TRUE`, then values are plotted above all points and bars.
`lm`	logical. If `TRUE`, the linear fit is plotted.
`cex.axis, cex.names, cex.values`	character scaling factor for numeric axis labels, names, and displayed values, respectively.
`inside`	logical. If `TRUE`, the lines which divide adjacent (non-stacked!) bars will be drawn. Only applies when `space = 0` (which it partly is when `beside = TRUE`).
`plot`	logical. If `FALSE`, nothing is plotted.
`axis.lty`	the graphics parameter `lty` applied to the axis and tick marks of the categorical (default horzontal) axis. Note that by default the axis is suppressed.
`plot.ci`	logical. If `TRUE`, confidence intervals are plotted over the bars. Note that if a stacked bar plot is generated, confidence intervals will not be plotted even if `plot.ci = TRUE`
`ci.l,ci.u`	The confidence intervals (ci.l = lower bound, ci.u = upper bound) to be plotted if `plot.ci` = `TRUE`. Values must have the same dim structure as `height`.
`ci.color`	the color for the confidence interval line segments
`ci.lty`	the line type for the confidence interval line segments
`ci.lwd`	the line width for the confidence interval line segments
`plot.grid`	if `TRUE` a lined grid will be plotted behind the bars
`grid.inc`	the number of grid increments to be plotted
`grid.lty`	the line type for the grid
`grid.lwd`	the line width for the grid
`grid.col`	the line color for the grid
`add`	logical, if `TRUE` add barplot to current plot.
`by.row`	Logical value. If `TRUE` the data matrix is organized with variables along rows rather than down colums.
`...`	further graphical parameters (`par`) are passed to `plot.window()`, `title()` and `axis`.

Details

Plot units are automatically scaled to SI units based on the maximum value present, according to the set of units specified by characters in the kmg parameter. These letters are interpreted as

P: peta = 1E15
T: tera = 1E12
G: giga = 1E09
M: mega = 1E06
k: kilo = 1E03
m: milli= 1E-03
u: micro= 1E-06
n: nano = 1E-09
p: pico = 1E-12
f: femto= 1E-15

with the default being "fpnumkMGTP" (all of these units). For example, if the largest value plotted is 1243000, it would be presented as 1.234M.

Value

A numeric vector (or matrix, when beside = TRUE), say mp, giving the coordinates of all the bar midpoints drawn, useful for adding to the graph.

If beside is true, use colMeans(mp) for the midpoints of each group of bars, see example.

Author(s)

Lodewijk Bonebakker bonebakker@comcast.net with modifications by Gregory R. Warnes greg@warnes.net. Based on barplot2().

Examples

data(VADeaths, package = "datasets")

     VADeaths <- cbind( Age=c(50,55,60,65,70), VADeaths)

     mp <- ooplot(VADeaths) # default
     mp <- ooplot(VADeaths, type="xyplot")  # same as default
     mp <- ooplot(VADeaths, type="linear")  # linear scale
     mp <- ooplot(VADeaths, type="linear", log="y") # log scale on y axis
     mp <- ooplot(VADeaths, type="barplot") # barplot
     mp <- ooplot(VADeaths, type="stackbar") # stacked


     tot <- colMeans(VADeaths[,-1])
     ooplot(VADeaths, 
             col = c("lightblue", "mistyrose", "lightcyan", "lavender"),
             legend = colnames(VADeaths)[-1], ylim = c(0, 100),
             type="barplot", cex.values=0.75)
     title(main = "Death Rates in Virginia", font.main = 4)


     ##
     ## Capability demo
     ##
     ## examples for the ooplot routine
     ##
     ## create some test data
     test1 <- data.frame(x=c(0,1,2,3,4), lin=c(0,1,2,3,4))
     test2 <- data.frame(x=c(0,1,2,3,4), par=c(0,1,4,9,16))
     test3 <- data.frame(x=c(-2,-1,0,1,2),y2=c(4,1,0,1,4))
     ## single line test example
     test1f <- test1
     ## two column example
     test2f <- merge(test1,test2,by.x="x",all=TRUE,sort=TRUE)
     ## three column example
     test3f <- merge(test2f,test3,by.x="x",all=TRUE,sort=TRUE)
     ## subset, single row, example
     test5r <- test3f[5,]  
     
     ##
     ## xyplot, linear, barplot, stackbar
     dev.off()
     mat <- matrix(c(1:16),4,4,byrow=TRUE)
     layout(mat)
     
     ooplot(test1f,type="barplot",col=c("red"))
     title(main="barplot")
     ooplot(test2f,type="barplot",col=c("red","blue"))
     ooplot(test3f,type="barplot",col=c("red","blue","green"))
     ooplot(test5r,type="barplot",col=c("red","blue","green"))
     
     ooplot(test1f,type="xyplot",col=c("red"))
     title(main="xyplot")
     ooplot(test2f,type="xyplot",col=c("red","blue"))
     ooplot(test3f,type="xyplot",col=c("red","blue","green"))
     ooplot(test5r,type="xyplot",col=c("red","blue","green"))
     
     ooplot(test1f,type="linear",col=c("red"))
     title(main="linear")
     ooplot(test2f,type="linear",col=c("red","blue"))
     ooplot(test3f,type="linear",col=c("red","blue","green"))
     ooplot(test5r,type="linear",col=c("red","blue","green"))
     
     ooplot(test1f,type="stackbar",col=c("red"))
     title(main="stackbar")
     ooplot(test2f,type="stackbar",col=c("red","blue"))
     ooplot(test3f,type="stackbar",col=c("red","blue","green"))
     ooplot(test5r,type="stackbar",col=c("red","blue","green"))

     # restore default layout (1 plot/page)
     layout(1)

gplots

Various R Programming Tools for Plotting Data

v3.1.1

GPL-2

Authors

Gregory R. Warnes [aut], Ben Bolker [aut], Lodewijk Bonebakker [aut], Robert Gentleman [aut], Wolfgang Huber [aut], Andy Liaw [aut], Thomas Lumley [aut], Martin Maechler [aut], Arni Magnusson [aut], Steffen Moeller [aut], Marc Schwartz [aut], Bill Venables [aut], Tal Galili [ctb, cre]

Initial release

2020-11-28