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pairs: Scatterplot Matrices

pairs

R Documentation

Scatterplot Matrices

Description

A matrix of scatterplots is produced.

Usage

pairs(x, ...)

## S3 method for class 'formula'
pairs(formula, data = NULL, ..., subset,
      na.action = stats::na.pass)

## Default S3 method:
pairs(x, labels, panel = points, ...,
      horInd = 1:nc, verInd = 1:nc,
      lower.panel = panel, upper.panel = panel,
      diag.panel = NULL, text.panel = textPanel,
      label.pos = 0.5 + has.diag/3, line.main = 3,
      cex.labels = NULL, font.labels = 1,
      row1attop = TRUE, gap = 1, log = "",
      horOdd = !row1attop, verOdd = !row1attop)

Arguments

`x`	the coordinates of points given as numeric columns of a matrix or data frame. Logical and factor columns are converted to numeric in the same way that `data.matrix` does.
`formula`	a formula, such as `~ x + y + z`. Each term will give a separate variable in the pairs plot, so terms should be numeric vectors. (A response will be interpreted as another variable, but not treated specially, so it is confusing to use one.)
`data`	a data.frame (or list) from which the variables in `formula` should be taken.
`subset`	an optional vector specifying a subset of observations to be used for plotting.
`na.action`	a function which indicates what should happen when the data contain `NA`s. The default is to pass missing values on to the panel functions, but `na.action = na.omit` will cause cases with missing values in any of the variables to be omitted entirely.
`labels`	the names of the variables.
`panel`	`function(x, y, ...)` which is used to plot the contents of each panel of the display.
`...`	arguments to be passed to or from methods. Also, graphical parameters can be given as can arguments to `plot` such as `main`. `par("oma")` will be set appropriately unless specified.
`horInd, verInd`	The (numerical) indices of the variables to be plotted on the horizontal and vertical axes respectively.
`lower.panel, upper.panel`	separate panel functions (or `NULL`) to be used below and above the diagonal respectively.
`diag.panel`	optional `function(x, ...)` to be applied on the diagonals.
`text.panel`	optional `function(x, y, labels, cex, font, ...)` to be applied on the diagonals.
`label.pos`	`y` position of labels in the text panel.
`line.main`	if `main` is specified, `line.main` gives the `line` argument to `mtext()` which draws the title. You may want to specify `oma` when changing `line.main`.
`cex.labels, font.labels`	graphics parameters for the text panel.
`row1attop`	logical. Should the layout be matrix-like with row 1 at the top, or graph-like with row 1 at the bottom? The latter (non default) leads to a basically symmetric scatterplot matrix.
`gap`	distance between subplots, in margin lines.
`log`	a character string indicating if logarithmic axes are to be used, see `plot.default` or a numeric vector of indices specifying the indices of those variables where logarithmic axes should be used for both x and y. `log = "xy"` specifies logarithmic axes for all variables.
`horOdd, verOdd`	`logical` (or integer) determining how the horizontal and vertical axis labeling happens. If true, the axis labelling starts at the first (from top left) row or column, respectively.

Details

The ijth scatterplot contains x[,i] plotted against x[,j]. The scatterplot can be customised by setting panel functions to appear as something completely different. The off-diagonal panel functions are passed the appropriate columns of x as x and y: the diagonal panel function (if any) is passed a single column, and the text.panel function is passed a single (x, y) location and the column name. Setting some of these panel functions to NULL is equivalent to not drawing anything there.

The graphical parameters pch and col can be used to specify a vector of plotting symbols and colors to be used in the plots.

The graphical parameter oma will be set by pairs.default unless supplied as an argument.

A panel function should not attempt to start a new plot, but just plot within a given coordinate system: thus plot and boxplot are not panel functions.

By default, missing values are passed to the panel functions and will often be ignored within a panel. However, for the formula method and na.action = na.omit, all cases which contain a missing values for any of the variables are omitted completely (including when the scales are selected).

Arguments horInd and verInd were introduced in R 3.2.0. If given the same value they can be used to select or re-order variables: with different ranges of consecutive values they can be used to plot rectangular windows of a full pairs plot; in the latter case ‘diagonal’ refers to the diagonal of the full plot.

Author(s)

Enhancements for R 1.0.0 contributed by Dr. Jens Oehlschlägel-Akiyoshi and R-core members.

References

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

Examples

pairs(iris[1:4], main = "Anderson's Iris Data -- 3 species",
      pch = 21, bg = c("red", "green3", "blue")[unclass(iris$Species)])

## formula method, "graph" layout (row 1 at bottom):
pairs(~ Fertility + Education + Catholic, data = swiss, row1attop=FALSE,
      subset = Education < 20, main = "Swiss data, Education < 20")

pairs(USJudgeRatings, gap=1/10) # (gap: not wasting plotting area)
## show only lower triangle (and suppress labeling for whatever reason):
pairs(USJudgeRatings, text.panel = NULL, upper.panel = NULL)

## put histograms on the diagonal
panel.hist <- function(x, ...)
{
    usr <- par("usr"); on.exit(par(usr))
    par(usr = c(usr[1:2], 0, 1.5) )
    h <- hist(x, plot = FALSE)
    breaks <- h$breaks; nB <- length(breaks)
    y <- h$counts; y <- y/max(y)
    rect(breaks[-nB], 0, breaks[-1], y, col = "cyan", ...)
}
pairs(USJudgeRatings[1:5], panel = panel.smooth,
      cex = 1.5, pch = 24, bg = "light blue", horOdd=TRUE,
      diag.panel = panel.hist, cex.labels = 2, font.labels = 2)

## put (absolute) correlations on the upper panels,
## with size proportional to the correlations.
panel.cor <- function(x, y, digits = 2, prefix = "", cex.cor, ...)
{
    usr <- par("usr"); on.exit(par(usr))
    par(usr = c(0, 1, 0, 1))
    r <- abs(cor(x, y))
    txt <- format(c(r, 0.123456789), digits = digits)[1]
    txt <- paste0(prefix, txt)
    if(missing(cex.cor)) cex.cor <- 0.8/strwidth(txt)
    text(0.5, 0.5, txt, cex = cex.cor * r)
}
pairs(USJudgeRatings, lower.panel = panel.smooth, upper.panel = panel.cor,
      gap=0, row1attop=FALSE)

pairs(iris[-5], log = "xy") # plot all variables on log scale
pairs(iris, log = 1:4, # log the first four
      main = "Lengths and Widths in [log]", line.main=1.5, oma=c(2,2,3,2))