ASEset-locationplot {AllelicImbalance} | R Documentation

## locationplot ASEset objects

### Description

plotting ASE effects over a specific genomic region

### Usage

    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,
      ...
    )

### 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.

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### 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='*')

[Package AllelicImbalance version 1.32.0 Index]