R: Plotting methods for interval objects

plot.Intervals {intervals} | R Documentation

## Plotting methods for interval objects

### Description

S3 methods for plotting `"Intervals"` and `"Intervals_full"` objects.

### Usage

    ## S3 method for class 'Intervals'
    plot(x, y, ...)
    ## S3 method for class 'Intervals_full'
    plot(
         x, y = NULL,
         axes = TRUE,
         xlab = "", ylab = "",
         xlim = NULL, ylim = NULL,
         col = "black", lwd = 1,
         cex = 1,
         use_points = TRUE,
         use_names = TRUE,
         names_cex = 1,
         ...
         )

    ## S4 method for signature 'Intervals,missing'
    plot(x, y, ...)
    ## S4 method for signature 'Intervals_full,missing'
    plot(x, y, ...)
    ## S4 method for signature 'Intervals,ANY'
    plot(x, y, ...)
    ## S4 method for signature 'Intervals_full,ANY'
    plot(x, y, ...)

### Arguments

`x` | An `"Intervals"` or `"Intervals_full"` object.
`y` | Optional vector of heights at which to plot intervals. If omitted, `y` will be automatically computed to generate a compact plot but with no overlap.
`axes` | As for `plot.default`.
`xlab` | As for `plot.default`.
`ylab` | As for `plot.default`.
`xlim` | As for `plot.default`.
`ylim` | If not explicitly supplied, `ylim` is set to the maximum value required for intervals which are visible for the given `xlim`.
`col` | Color used for segments and endpoint points and interiors. Recycled if necessary.
`lwd` | Line width for segments. See `par`.
`cex` | Endpoint magnification. Only relevant if `use_points = TRUE`. See `par`.
`use_points` | Should points be plotted at interval endpoints?
`use_names` | Should `rownames(x)` by used for segment labels in the plot?
`names_cex` | Segment label magnification. Only relevant if `use_names = TRUE`.
`...` | Other arguments for `plot.default`.

### Details

Intervals with `NA` for either endpoint are not plotted. Vertical placement is on the integers, beginning with 0.

### Value

None.

### Examples

    # Note plot symbol for empty interval in 'from'.

    from <- Intervals(
                      matrix(
                             c(
                                2,  8,
                                8,  9,
                                6,  9,
                               11, 12,
                                3,  3
                               ),
                             ncol = 2, byrow = TRUE
                             ),
                      closed = c( FALSE, TRUE ),
                      type = "Z"
                      )

    rownames(from) <- c("a","b","c","d","e")

    to <- Intervals(
                    matrix(
                           c(
                             2,  8,
                             3,  4,
                             5, 10
                             ),
                           ncol = 2, byrow = TRUE
                           ),
                    closed = c( FALSE, TRUE  ),
                    type = "Z"
                    )

    rownames(to) <- c("x","y","z")

    empty(from)

    plot(
         c(from,to),
         col = rep(1:2, c(nrow(from), nrow(to)))
         )

    legend("topright", c("from","to"), col=1:2, lwd=1)

    # More intervals. The maximal height shown is adapted to the plotting
    # window.

    B <- 10000
    left <- runif( B, 0, 1e5 )
    right <- left + rexp( B, rate = 1/10 )
    x <- Intervals( cbind( left, right ) )

    plot(x, use_points=FALSE)
    plot(x, use_points=FALSE, xlim = c(0, 500))

[Package intervals version 0.15.2 Index]