ASEset-barplot {AllelicImbalance} | R Documentation

## 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, ...)

    ## 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,
      ...
    )

### 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.

`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.

### Author(s)

Jesper R. Gadin, Lasse Folkersen

### See Also

- The `ASEset` class which the barplot function can be called up on.

### Examples

    data(ASEset)
    barplot(ASEset[1])

[Package AllelicImbalance version 1.25.2 Index]