AllelicImbalance (version 1.10.2)

ASEset-locationplot: locationplot ASEset objects

Description

plotting ASE effects over a specific genomic region

Usage

locationplot(x, ...)
"locationplot"(x, type = "fraction", strand = "*", yaxis = TRUE, xaxis = FALSE, xlab = FALSE, ylab = TRUE, xlab.text = "", ylab.text = "", legend.colnames = "", size = c(0.8, 1), main = NULL, pValue = FALSE, cex.main = 0.7, cex.ylab = 0.6, cex.legend = 0.5, OrgDb = NULL, TxDb = NULL, verbose = TRUE, top.fraction.criteria = "maxcount", allow.whole.chromosome = FALSE, ...)

Arguments

x

an ASEset object.

...

arguments passed on to barplot function

type

'fraction' or 'count'

strand

'+','-','*' or 'both'. This argument determines which strand is plotted. See getAlleleCounts for more information on strand.

yaxis

wheter the y-axis is to be displayed or not

xaxis

wheter the x-axis is to be displayed or not

xlab

showing labels for the tic marks

ylab

showing labels for the tic marks

xlab.text

xlab text

ylab.text

ylab text

legend.colnames

gives colnames to the legend matrix

size

will give extra space in the margins of the inner plots

main

text to use as main label

pValue

Display p-value

cex.main

set main label size

cex.ylab

set ylab label size

cex.legend

set legend label size

OrgDb

an OrgDb object from which to plot a gene map. If given together with argument TxDb this will only be used to extract genesymbols.

TxDb

a TxDb object from which to plot an exon map.

verbose

Setting verbose=TRUE gives details of procedure during function run

top.fraction.criteria

'maxcount', 'ref' or 'phase'

allow.whole.chromosome

logical, overrides 200kb region limit, defaults to FALSE

Details

The locationplot methods visualises how fractions are distributed over a larger region of genes on one chromosome. It takes and ASEset object as well as additional information on plot type (see barplot), strand type (see getAlleleCounts), colouring, as well as annotation. The annotation is taken either from the bioconductor OrgDb-sets, the TxDb sets or both. It is obviously important to make sure that the genome build used is the same as used in aligning the RNA-seq data.

See Also

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

Examples

data(ASEset)
locationplot(ASEset)

#SNPs are plotted in the order in which they are found. 
#This can be sorted according to location as follows:
locationplot(ASEset[order(start(rowRanges(ASEset))),])

#for ASEsets with fewer SNPs the 'count' type plot is
# useful for detailed visualization.
locationplot(ASEset,type='count',strand='*')