stat_table-method: Tabulate a GRanges object

In ggbio: Visualization tools for genomic data

Description

Tabulate a GRanges object

Usage

## S4 method for signature 'GRanges'
stat_table(data, ..., xlab, ylab, main,
            geom = NULL,stat = NULL)
## S4 method for signature 'GRangesList'
stat_table(data, ..., xlab, ylab, main,
            facets = NULL, geom = NULL)

Arguments

data	A GRanges or data.frame object.
...	Extra parameters such as aes() passed to geom_rect, geom_alignment, or geom_segment.
xlab	Label for x
ylab	Label for y
main	Title for plot.
facets	Faceting formula to use.
geom	The geometric object to use display the data.
stat	The geometric object to use display the data.

Value

A 'Layer'.

Author(s)

Tengfei Yin

Examples

##  load
set.seed(1)
N <- 100
require(ggbio)
require(GenomicRanges)
##  simul
## ======================================================================
##  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))

gr <- c(gr[seqnames(gr) == "chr1"][sample(1:10, size = 1e4, replace = TRUE)],gr)

##  default
ggplot(gr) + stat_table()
ggplot(gr) + stat_table(geom = "segment", aes(y = ..score.., color = ..score..))
ggplot(gr) + stat_table(aes(color = score))

ggbio documentation built on Nov. 8, 2020, 5:04 p.m.