SpTrellis-class {ShortRead} | R Documentation

## Class "SpTrellis"

### Description

A reference class to manage the trellis graphics related component of the `Snapshot` functionality for visualization of genomic data.

### Usage

    SpTrellis(trellis, debug_enabled=FALSE)

### Arguments

`trellis` | A trellis object for storing the plot of the genome area being visualized.
`debug_enabled` | `logical(1)` indicating whether class methods should report debugging information to the user.

### Fields

`trellis`:

  Object of class `trellis` for storing the plot information.

debug_enabled

  `logical(1)` indicating whether class methods should report debugging information to the user.

### Methods

zi

  `signature(x="SpTrellis")`: zoom in

zo

  `signature(x="SpTrellis")`: zoom out

right

  `signature(x="SpTrellis")`: shift to the right

left

  `signature(x="SpTrellis")`: shift to the left

restore

  `signature(x="SpTrellis")`: restore to the original plot

show

  `signature(x="SpTrellis")`: show the current plot

update

  `signature(x="SpTrellis")`: update the trellis parameters of the `SpTrellis` object.

### Author(s)

Chao-Jen cwon2@fhcrc.org

### See Also

`Snapshot`

### Examples

    col <- c("#66C2A5", "#FC8D62")
    x = numeric(1000)
    x[sample(1000, 100)] <- abs(rnorm(100))
    df <- data.frame(x = c(x, -x), pos = seq(1, 1e5, length.out=1000),
                     group = rep(c("positive", "negative"), each=1000))
    cv <- lattice::xyplot(x ~ pos, df, group=group, type="s",
        col=col, main="yeast chrI:1 - 2e5",
        ylab="Coverage", xlab="Coordinate",
        scales=list(y=list(tck=c(1,0)),
                    x=list(rot=45, tck=c(1,0), tick.number=20)),
        panel=function(...) {
                lattice::panel.xyplot(...)
                lattice::panel.grid(h=-1, v=20)
                lattice::panel.abline(a=0, b=0, col="grey")
        })
    s <- SpTrellis(cv)
    s
    zi(s)
    zi(s)
    left(s)
    right(s)
    zo(s)
    restore(s)

[Package ShortRead version 1.52.0 Index]