geom_arch-method: Arch geoms for GRanges object

In lawremi/ggbio: Visualization tools for genomic data

Arch geoms for GRanges object

Description

Show interval data as arches.

Usage

## S4 method for signature 'data.frame'
geom_arch(data, ..., n = 25, max.height = 10)


## S4 method for signature 'GRanges'
geom_arch(data, ..., xlab, ylab, main, facets = NULL,
                 rect.height = 0, n = 25, max.height = 10)

Arguments

data	A GRanges or data.frame object.
...	Extra parameters passed to autoplot function, aes mapping support height, x, xend. xstart of the arches xendend of the arches heightheight of arches
xlab	Label for x
ylab	Label for y
main	Title for plot.
n	Integer values at which interpolation takes place to create 'n' equally spaced points spanning the interval ['min(x)', 'max(x)'].
facets	Faceting formula to use.
rect.height	When data is GRanges, this padding the arches from original y value to allow users putting arches 'around' the interval rectangles.
max.height	Max height of all arches.

Details

To draw a interval data as arches, we need to provide a special geom for this purpose. Arches is popular in gene viewer or genomoe browser, when they try to show isoforms or gene model.geom_arch, just like any other geom_* function in ggplot2, you can pass aes() to it to map variable to height of arches.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

set.seed(1)
N <- 100
library(GenomicRanges)

## =======================================
##  simmulated GRanges
## =======================================
gr <- GRanges(seqnames = 
              sample(c("chr1", "chr2", "chr3"),
                     size = N, replace = TRUE),
              IRanges(
                      start = sample(1:300, size = N, replace = TRUE),
                      width = sample(70:75, size = N,replace = TRUE)),
              strand = sample(c("+", "-", "*"), size = N, 
                replace = TRUE),
              value = rnorm(N, 10, 3), score = rnorm(N, 100, 30),
              sample = sample(c("Normal", "Tumor"), 
                size = N, replace = TRUE),
              pair = sample(letters, size = N, 
                replace = TRUE))

## =======================================
##  default
## =======================================
ggplot(gr) + geom_arch()
# or
ggplot() + geom_arch(gr)

## =======================================
##  facetting and aesthetics
## =======================================
ggplot(gr) + geom_arch(aes(color = value, height = value, size = value),
                     alpha = 0.2, facets = sample ~ seqnames)

lawremi/ggbio documentation built on Nov. 1, 2023, 2:40 p.m.