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])