ASEset-barplot: barplot ASEset objects

In AllelicImbalance: Investigates Allele Specific Expression

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, ...)

## S4 method for signature 'ASEset'
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.

Author(s)

Jesper R. Gadin, Lasse Folkersen

See Also

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

Examples

data(ASEset)
barplot(ASEset[1])

AllelicImbalance documentation built on Nov. 8, 2020, 6:52 p.m.