stat_slice {ggbio} | R Documentation

## Slice Rle/RleList to view them as bar or heatmap.

### Description

Slice Rle/RleList to different view by set lower or other parameters, then view summary for all those viewed region.

### Usage

    ## S4 method for signature 'Rle'
    stat_slice(data, ...,
              xlab, ylab, main,
              na.rm = FALSE,
              geom = NULL,
              lower=-Inf, upper=Inf,
              includeLower=TRUE, includeUpper=TRUE,
              rangesOnly = FALSE,
              type = c("viewSums","viewMins",
              "viewMaxs", "viewMeans"))

    ## S4 method for signature 'RleList'
    stat_slice(data, ...,
              xlab, ylab, main,
              indName = "sample",
              na.rm = FALSE,
              geom = NULL,
              lower=-Inf, upper=Inf,
              includeLower=TRUE, includeUpper=TRUE,
              rangesOnly = FALSE,
              type = c("viewSums","viewMins",
                       "viewMaxs", "viewMeans"))

### Arguments

`data` | a `data.frame` or `Rle` or `RleList` object.
`...` | arguments passed to aesthetics mapping.
`xlab` | x label.
`ylab` | y label.
`main` | title.
`indName` | when faceted by a `RleList`, name used for labeling faceted factor. Default is 'sample'.
`geom` | geometric types.
`type` | statistical summary method used within bins, shown as bar height or heatmap colors.
`na.rm` | logical value, default `FALSE`, passed to function like `viewMaxs` for statistical summary computation.
`lower` | passed to `slice`.
`upper` | passed to `slice`.
`includeLower` | passed to `slice`.
`includeUpper` | passed to `slice`.
`rangesOnly` | passed to `slice`.

### Value

a ggplot object.

### Author(s)

Tengfei Yin

### See Also

`slice`

### Examples

    library(IRanges)
    lambda <- c(rep(0.001, 4500), seq(0.001, 10, length = 500),
                seq(10, 0.001, length = 500))
    xVector <- rpois(1e4, lambda)
    xRle <- Rle(xVector)
    xRleList <- RleList(xRle, 2L * xRle)

    ggplot(xRle) + stat_slice(lower = 5)
    ggplot(xRle) + stat_slice(lower = 5, geom = "bar")
    ggplot(xRle) + stat_slice(lower = 5, geom = "heatmap")

    p1 <- ggplot(xRle) + stat_slice(type = "viewMeans", lower = 5,
                                geom = "bar")
    p2 <- ggplot(xRle) + stat_slice(type = "viewSums", lower = 5,
                                geom = "bar")
    ## y scale are different.
    tracks(viewMeans = p1, viewSums = p2)

    ggplot(xRleList) + stat_slice(lower = 5)
    ggplot(xRleList) + stat_slice(lower = 5, geom = "bar")
    ggplot(xRleList) + stat_slice(lower = 5, geom = "heatmap")

    p1 <- ggplot(xRleList) + stat_slice(type = "viewMeans", lower = 5,
                                geom = "bar")
    p2 <- ggplot(xRleList) + stat_slice(type = "viewSums", lower = 5,
                                geom = "bar")
    ## y scale are different.
    tracks(viewMeans = p1, viewSums = p2)

[Package ggbio version 1.28.5 Index]