ASEset-barplot: barplot ASEset objects
In pappewaio/AllelicImbalance: Investigates Allele Specific Expression

Description Usage Arguments Details Author(s) See Also Examples

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.

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,
  ...
)

`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

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.

Jesper R. Gadin, Lasse Folkersen