R: Binning method

stat_bin {ggbio}

R Documentation

Binning method

Description

Binning method especially for Rle and RleList, for data.frame it's just calling ggplot2::stat_bin.

Usage

## S4 method for signature 'data.frame'
stat_bin(data, ...)

## S4 method for signature 'Rle'
stat_bin(data, ..., binwidth, nbin = 30,
         xlab, ylab, main, geom = c("bar", "heatmap"),
         type = c("viewSums","viewMins",
                                  "viewMaxs", "viewMeans"))
## S4 method for signature 'RleList'
stat_bin(data, ..., binwidth, nbin = 30,
          xlab, ylab, main,
          indName = "sample",
          geom = c("bar", "heatmap"),
          type = c("viewSums","viewMins",
          "viewMaxs", "viewMeans"))

Arguments

`data`	a `data.frame` or `Rle` or `RleList` object.
`...`	arguments passed to aesthetics mapping.
`binwidth`	width of the bins.
`nbin`	number of bins.
`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.

Value

a ggplot object.

Author(s)

Tengfei Yin

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() + stat_bin(xRle)

## Default use binwidth: range/30

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ggplot(xRle) + stat_bin()

## Default use binwidth: range/30

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ggplot(xRle) + stat_bin(nbin = 100)

## Default use binwidth: range/100

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ggplot(xRle) + stat_bin(binwidth = 200)

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p1 <- ggplot(xRle) + stat_bin(type = "viewMeans")

## Default use binwidth: range/30

p2 <- ggplot(xRle) + stat_bin(type = "viewSums")

## Default use binwidth: range/30

## y scale are different.
tracks(viewMeans = p1, viewSums = p2)

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ggplot(xRle) + stat_bin(geom = "heatmap")

## Default use binwidth: range/30

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ggplot(xRle) + stat_bin(nbin = 100, geom = "heatmap")

## Default use binwidth: range/100

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ggplot(xRle) + stat_bin(binwidth = 200, geom = "heatmap")

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## for RleList
ggplot(xRleList) + stat_bin()

## Default use binwidth: range/30

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ggplot(xRleList) + stat_bin(nbin = 100)

## Default use binwidth: range/100

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ggplot(xRleList) + stat_bin(binwidth = 200)

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p1 <- ggplot(xRleList) + stat_bin(type = "viewMeans")

## Default use binwidth: range/30

p2 <- ggplot(xRleList) + stat_bin(type = "viewSums")

## Default use binwidth: range/30

## y scale are different.
tracks(viewMeans = p1, viewSums = p2)

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ggplot(xRleList) + stat_bin(geom = "heatmap")

## Default use binwidth: range/30

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ggplot(xRleList) + stat_bin(nbin = 100, geom = "heatmap")

## Default use binwidth: range/100

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ggplot(xRleList) + stat_bin(binwidth = 200, geom = "heatmap")

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[Package ggbio version 1.5.20 ]