AllelicImbalance (version 1.10.2)

ASEset-barplot: barplot ASEset objects

Description

Generates barplots for ASEset objects. Two levels of plotting detail are provided: a detailed barplot of read counts by allele useful for fewer samples and SNPs, and a less detailed barplot of the fraction of imbalance, useful for more samples and SNPs.

Usage

barplot(height, ...)
"barplot"(height, type = "count", sampleColour.top = NULL, sampleColour.bot = NULL, legend = TRUE, pValue = TRUE, strand = "*", testValue = NULL, testValue2 = NULL, OrgDb = NULL, TxDb = NULL, annotationType = c("gene", "exon", "transcript"), main = NULL, ylim = NULL, yaxis = TRUE, xaxis = FALSE, ylab = TRUE, ylab.text = NULL, xlab.text = "samples", xlab = TRUE, legend.colnames = "", las.ylab = 1, las.xlab = 2, cex.main = 1, cex.pValue = 0.7, cex.ylab = 0.7, cex.xlab = 0.7, cex.legend = 0.6, add = FALSE, lowerLeftCorner = c(0, 0), size = c(1, 1), addHorizontalLine = 0.5, add.frame = TRUE, filter.pValue.fraction = 0.99, legend.fill.size = 1, legend.interspace = 1, verbose = FALSE, top.fraction.criteria = "maxcount", cex.annotation = 0.7, ypos.annotation = 0, annotation.interspace = 1, ...)

Arguments

height

An ASEset object

...

for simpler generics when extending function

type

'count' or 'fraction'

sampleColour.top

User specified colours for top fraction

sampleColour.bot

User specified colours for bottom fraction

legend

Display legend

pValue

Display p-value

strand

four options, '+', '-', 'both' or '*'

testValue

if set, a matrix or vector with user p-values

testValue2

if set, a matrix or vector with user p-values

OrgDb

an OrgDb object which provides annotation

TxDb

a TxDb object which provides annotation

annotationType

select one or more from 'gene','exon','transcript','cds'.

main

text to use as main label

ylim

set plot y-axis limit

yaxis

wheter the y-axis is to be displayed or not

xaxis

wheter the x-axis is to be displayed or not

ylab

showing labels for the tic marks

ylab.text

ylab text

xlab.text

xlab text

xlab

showing labels for the tic marks

legend.colnames

gives colnames to the legend matrix

las.ylab

orientation of ylab text

las.xlab

orientation of xlab text

cex.main

set main label size (max 2)

cex.pValue

set pValue label size

cex.ylab

set ylab label size

cex.xlab

set xlab label size

cex.legend

set legend label size

add

boolean indicates if a new device should be started

lowerLeftCorner

integer that is only useful when add=TRUE

size

Used internally by locationplot. Rescales each small barplot window

addHorizontalLine

adds a horizontal line that marks the default fraction of 0.5 - 0.5

add.frame

boolean to give the new plot a frame or not

filter.pValue.fraction

numeric between 0 and 1 that filter away pValues where the main allele has this frequency.

legend.fill.size

size of the fill/boxes in the legend (default:NULL)

legend.interspace

set legend space between fills and text

verbose

Makes function more talkative

top.fraction.criteria

'maxcount', 'ref' or 'phase'

cex.annotation

size of annotation text

ypos.annotation

relative ypos for annotation text

annotation.interspace

space between annotation text

Details

filter.pValue.fraction is intended to remove p-value annotation with very large difference in frequency, which could just be a sequencing mistake. This is to avoid p-values like 1e-235 or similar.

sampleColourUser specified colours, either given as named colours ('red', 'blue', etc) or as hexadecimal code. Can be either length 1 for all samples, or else of a length corresponding to the number of samples for individual colouring.

See Also

• The ASEset class which the barplot function can be called up on.

Examples

data(ASEset)
barplot(ASEset[1])