ASEset-barplot {AllelicImbalance} | R Documentation |
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 |
... |
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 |
|
lowerLeftCorner |
integer that is only useful when |
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 |
|
filter.pValue.fraction |
|
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.
sampleColour
User 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
The ASEset
class which the barplot
function can be called up on.
data(ASEset) barplot(ASEset[1])