plot.Intervals: Plotting methods for interval objects

In intervals: Tools for Working with Points and Intervals

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))

intervals documentation built on Sept. 11, 2024, 9:05 p.m.