plotGenomeBrowser: #' Plot a genome browser view #' #' Plot a simple genome...

In chromstaR: Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data

Description

Plot a simple genome browser view of chromstaR-objects. This is useful for scripted genome browser snapshots.

Usage

plotGenomeBrowser(
  model,
  chr,
  start,
  end,
  style = "peaks",
  peakHeight = 0.2,
  peakColor = "blue",
  same.yaxis = TRUE
)

Arguments

model	A uniHMM, multiHMM or combinedMultiHMM object or file that contains such an object.
chr, start, end	Chromosome, start and end coordinates for the plot.
style	One of c('peaks', 'density').
peakHeight	Height of the peak track relative to the count track.
peakColor	Color for the peak track.
same.yaxis	Whether or not the plots for the same mark have the same y-axis.

Value

A list() of ggplot objects.

Examples

## Get an example uniHMM ##
file <- system.file("data","H3K27me3-BN-rep1.RData", package="chromstaR")
model <- get(load(file))
plotGenomeBrowser(model, chr='chr12', start=1, end=1e6, style='peaks',
                 peakHeight=0.1)
                 
## Get an example multiHMM ##
file <- system.file("data","multivariate_mode-combinatorial_condition-SHR.RData",
                    package="chromstaR")
model <- get(load(file))
plotGenomeBrowser(model, chr='chr12', start=1, end=1e6, style='peaks',
                 peakHeight=0.1)
                 
## Get an example combinedMultiHMM ##
file <- system.file("data","combined_mode-differential.RData",
                    package="chromstaR")
model <- get(load(file))
plotlist <- plotGenomeBrowser(model, chr='chr12', start=1, end=1e6, style='peaks',
                 peakHeight=0.1)

chromstaR documentation built on Nov. 8, 2020, 8:29 p.m.