R: Scatterplot Matrices

pairs {graphics} | 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, ...,
          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 = "")

### 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.
`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?
`gap` | distance between subplots, in margin lines.
`log` | a character string indicating if logarithmic axes are to be used: see `plot.default`. `log = "xy"` specifies logarithmic axes for all variables.

### 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).

### Author(s)

Enhancements for R 1.0.0 contributed by Dr. Jens Oehlschlaegel-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
    pairs(~ Fertility + Education + Catholic, data = swiss,
          subset = Education < 20, main = "Swiss data, Education < 20")

    pairs(USJudgeRatings)
    ## 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",
          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)

    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))

[Package graphics version 3.1.2 Index]