plotChimericReads {R453Plus1Toolbox} | R Documentation

## Plots chimeric reads

### Description

This function plots a given set of aligned chimeric reads along a reference sequence. It plots the breakpoints of translations or inversions and marks deletions, insertions and mismatches. Optionally, it displays all base pairs in a given region around the breakpoint.

### Usage

    plotChimericReads(brpData, geneSymbols=FALSE, plotMut=TRUE, plotBasePairs=FALSE, maxBasePairs=50, legend=FALSE, title="",
        col=c("red", "green", "black", "orange"))

### Arguments

`brpData` | A `Breakpoints` object containing the consensus breakpoint of all reads and the consensus reference sequence as returned by the methods `detectBreakpoints` and `mergeBreakpoints`. Since only one plot is made, the function will only work for objects of class `Breakpoints` having length one.
`geneSymbols` | Boolean value whether to automatically load and plot the gene symbols from the Ensembl database. Additionally, `geneSymbols` can be a vector of two strings for an own annotation.
`plotMut` | Boolean value whether to mark deletions, insertions and mismatches.
`plotBasePairs` | Optionally, `plotChimericReads` displays all base pairs in a given region around the breakpoint (see maxBasePairs).
`maxBasePairs` | The maximum number of base pairs to be plotted. Only used in conjunction with `plotBasePairs=TRUE`.
`legend` | A logical value (TRUE/FALSE) whether to plot a legend that explains the colouration of the insertions, deletions, mismatches and breakpoints.
`title` | A title for the plot.
`col` | A vector of four colours to draw insertions, deletions, mismatches and breakpoints. In this order, the default colours are "red", "green", "black" and "orange" (use `colours()` to see a list of possible values).

### Details

This method is intended to be run after the pipeline for structural variant detection. Therefore, see the methods `filterChimericReads`, `detectBreakpoints` and `mergeBreakpoints` to correctly preprocess your alignment before running `plotChimericReads`.

### Note

It is recommended to first create and resize the output device (e.g. the plotting window or a pdf file) before plotting. For example, on Unix systems you may try `X11(width=w, height=h)` or `pdf(file="plotChimericReads.pdf", width=w, height=h)` for some window width w (e.g. w=12) and window height h (e.g. h=6).

### Author(s)

Christoph Bartenhagen

### See Also

`Breakpoints-class`, `detectBreakpoints`, `mergeBreakpoints`

### Examples

    # load breakpoint data containing twelve chimeric reads describing an inversion in chromosome 16
    data("breakpoints")
    breakpoints

    # standard plot
    # (only arrangement of reads plotted; breakpoints in orange, deletions
    # in red, insertions in green and mismatches in black by default)
    plotChimericReads(breakpoints)

    # plot base pairs in the breakpoint region (+/- 32bp)
    ## Not run: plotChimericReads(breakpoints, plotBasePairs=TRUE, maxBasePairs=32)

    # use custom colours and display a legend:
    # deletions="brown", insertions="blue", mismatches="yellow", breakpoints="gray"
    plotChimericReads(breakpoints, col=c("brown", "blue", "yellow", "gray"), legend=TRUE)

[Package R453Plus1Toolbox version 1.40.0 Index]