stat_table-method: Tabulate a GRanges object

Description Usage Arguments Value Author(s) Examples

Description

Tabulate a GRanges object

Usage

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## 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

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##  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 Aug. 24, 2018, 6 p.m.