locationplot: locationplot ASEset objects
In AllelicImbalance: Investigates Allele Specific Expression

Description Usage Arguments Details Author(s) See Also Examples

plotting ASE effects over a specific genomic region

locationplot(x, ...)

## S4 method for signature 'ASEset'
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,
  ...
)

`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

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.

Jesper R. Gadin, Lasse Folkersen

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

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='*')