draw.pileup {Rgb} | R Documentation

## Pileup plot of a BAM track

### Description

This function draws a slice of a sequence pileup, highlighting polymorphisms.

### Usage

      draw.pileup(slice, start, end, ylim = NA, bty = "o", label = TRUE, labelCex = 0.75,
        bases = c(A = "#44CC44", C = "#4444CC", G = "#FFCC00", T = "#CC4444"),
        maxRange = 500, cex.lab = 1, alphaOrder = 3, alphaMin = 0.1, ...)

### Arguments

`slice` | An integer matrix of read counts, with nucleotides in rows and positions in columns. Both dimensions must be named.
`start` | Single integer value, the left boundary of the window, in base pairs.
`end` | Single integer value, the right boundary of the window, in base pairs.
`ylim` | See `plot.default`. `NA` will compute a dynamic ylim fiting the data.
`bty` | A character string which determined the type of box which is drawn about plots. If bty is one of "o" (the default), "l", "7", "c", "u", or "]" the resulting box resembles the corresponding upper case letter. A value of "n" suppresses the box. See `par`.
`label` | Single logical value, whether to print nucleotide on bars or not.
`labelCex` | Single numeric value, character expansion factor for labels.
`bases` | Named character vector, defining the color to use for each nucleotide.
`maxRange` | Single integer value, nothing will be ploted if the plot window is wider by this value (in bases).
`cex.lab` | The relative character size of x and y axis labels (default: 1). See `par`.
`alphaOrder` | Single numeric value, the order of the formula controlling the transparency. Increase this value to increase sensitivity to rare variants.
`alphaMin` | Single numeric value, the minimal intensity in the formula controlling the transparency (between 0 and 1). Perfectly homozyguous positions will typically use this intensity of color.
`...` | Further arguments to be passed to `draw.bg`.

### Author(s)

Sylvain Mareschal

### See Also

`track.bam-class`

`draw.bg`, `draw.boxes`, `draw.steps`, `draw.hist`, `draw.points`, `draw.seq`

[Package Rgb version 1.6.1 Index]