geom_rect-method: Rect geoms for GRanges object

In lawremi/ggbio: Visualization tools for genomic data

Rect geoms for GRanges object

Description

Show interval data as rectangle.

Usage

## S4 method for signature 'ANY'
geom_rect(data, ...)
## S4 method for signature 'GRanges'
geom_rect(data,..., xlab, ylab, main,
          facets = NULL, stat = c("stepping", "identity"),
          rect.height = NULL,
          group.selfish = TRUE)

Arguments

data	Typically a GRanges or data.frame object. When it's data.frame, it's simply calling ggplot2::geom_rect.
...	Extra parameters such as aes() or color, size passed.
xlab	Label for x
ylab	Label for y
main	Title for plot.
facets	Faceting formula to use.
stat	Character vector specifying statistics to use. "stepping" with randomly assigned stepping levels as y varialbe. "identity" allow users to specify y value in aes.
rect.height	Half height of the arrow body.
group.selfish	Passed to addStepping, control whether to show each group as unique level or not. If set to FALSE, if two groups are not overlapped with each other, they will probably be layout in the same level to save space.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

set.seed(1)
N <- 100
require(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))



## ======================================================================
##  data.frame call ggplot2::geom_rect
## ======================================================================
ggplot() + geom_rect(data = mtcars, aes(xmin = mpg, ymin = wt, xmax = mpg + 10, ymax = wt + 0.2,
                       fill = cyl))



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


## ======================================================================
##  facetting and aesthetics
## ======================================================================
ggplot(gr) + geom_rect(facets = sample ~ seqnames, aes(color = strand, fill = strand))


## ======================================================================
##  stat:identity
## ======================================================================
ggplot(gr) + geom_rect(stat = "identity", aes(y = value))


## ======================================================================
##  stat:stepping
## ======================================================================
ggplot(gr) + geom_rect(stat = "stepping", aes(y = value, group = pair))


## ======================================================================
##  group.selfish controls when 
## ======================================================================
ggplot(gr) + geom_rect(stat = "stepping", aes(y = value, group = pair), group.selfish = FALSE)

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