geom_bar-method: Segment geoms for GRanges object

In tengfei/ggbio: Visualization tools for genomic data

Segment geoms for GRanges object

Description

Show interval data as vertical bar, width equals to interval width and use 'score' or specified 'y' as y scale.

Usage

## S4 method for signature 'ANY'
geom_bar(data, ...)
## S4 method for signature 'GRanges'
geom_bar(data,..., xlab, ylab, main)

Arguments

data	Typically a GRanges or data.frame object.
...	Extra parameters such as aes() or color, size passed.
xlab	Label for x
ylab	Label for y
main	Title for plot.

Details

Useful for showing bed like files, when imported as GRanges, have a extra 'score' column, use it as default y, you could also specify y by using aes(y = ).

Value

A 'Layer'.

Examples

## load
library(GenomicRanges)

## simul
set.seed(123)
gr.b <- GRanges(seqnames = "chr1", IRanges(start = seq(1, 100, by = 10),
                  width = sample(4:9, size = 10, replace = TRUE)),
                score = rnorm(10, 10, 3), value = runif(10, 1, 100))
gr.b2 <- GRanges(seqnames = "chr2", IRanges(start = seq(1, 100, by = 10),
                  width = sample(4:9, size = 10, replace = TRUE)),
                score = rnorm(10, 10, 3), value = runif(10, 1, 100))
gr.b <- c(gr.b, gr.b2)
## default use score as y

## bar
ggplot(gr.b) + geom_bar(aes(fill = value))
## or
ggplot() + geom_bar(gr.b, aes(fill = value))
ggplot(gr.b) + geom_bar(aes(y = value))
## equal to
autoplot(gr.b, geom = "bar")

tengfei/ggbio documentation built on Nov. 5, 2023, 6:17 a.m.