plotTranscript {riboSeqR} | R Documentation

## Plots ribosome footprint abundance and mRNA coverage (if available) for a specific transcript.

### Description

Abundances of ribosomal footprints of a given size class are plotted on a transcript. The footprints are colour coded according to the first base of the transcript, and not any coding start site, to allow for multiple coding start sites on a given transcript. Coding regions may simultaneously be plotted and colour coded under the same scheme.

### Usage

    plotTranscript(transcript, coordinates, annotation, riboData, length =
    27, frameShift = 0, cap, riboScale, rnaScale, xlim, main, note = "",
    libScales, ...)

### Arguments

`transcript` | The name of the transcript to be plotted.
`coordinates` | A GRanges object containing any coding regions on the transcript.
`annotation` | A GRanges object containing annotated coding coordinates to be plotted as bars above the figure.
`riboData` | A `riboData` object containing the ribosome footprint (and optionally, RNA-seq) data.
`length` | Size class of ribosome footprint data to be plotted.
`frameShift` | Frameshift for the ribosome footprint data. See Details.
`cap` | Cap on the largest value that will be plotted as an abundance of the ribosome footprint data.
`riboScale` | Scale to be used on the ribosome footprint axis.
`rnaScale` | Scale to be used on the RNA-seq coverage axis.
`xlim` | Limits of the bases of the transcript to be plotted (i.e., the x-axis). If missing, the full transcript will be plotted.
`main` | Optional title for the plot.
`note` | Additional note to be added to plot titles (in addition to transcript and sample names).
`libScales` | If supplied, library scaling factors for normalisation of ribosomal and RNA counts (see `libScales`).
`...` | Additional arguments to be passed to plotting function.

### Details

The readingFrame value allows the colour-coding of the ribosome footprints to be shifted so that the colours of the coding sequences match the colours of the ribosome footprint data. E.g., if 28-mers are predominantly in frame 2 relative to coding start, a value of ‘readingFrame=2’ will ensure that 28-mers in a coding region will take the same colour as that coding region if they are in the correct relative frame.

### Value

NULL; plotting function.

### Author(s)

Thomas J. Hardcastle

### Examples

    #ribosomal footprint data
    datadir <- system.file("extdata", package = "riboSeqR")
    ribofiles <- paste(datadir,
                       "/chlamy236_plus_deNovo_plusOnly_Index", c(17,3,5,7), sep = "")
    rnafiles <- paste(datadir,
                      "/chlamy236_plus_deNovo_plusOnly_Index", c(10,12,14,16), sep = "")

    riboDat <- readRibodata(ribofiles, rnafiles, replicates = c("WT", "WT",
    "M", "M"))

    # CDS coordinates
    chlamyFasta <- paste(datadir, "/rsem_chlamy236_deNovo.transcripts.fa", sep = "")
    fastaCDS <- findCDS(fastaFile = chlamyFasta,
                        startCodon = c("ATG"),
                        stopCodon = c("TAG", "TAA", "TGA"))

    # frame calling
    fCs <- frameCounting(riboDat, fastaCDS)

    # analysis of frame shift for 27 and 28-mers.
    fS <- readingFrame(rC = fCs, lengths = 27:28)

    # filter coding sequences. 27-mers are principally in the 1-frame,
    # 28-mers are principally in the 0-frame relative to coding start (see
    # readingFrame function).

    ffCs <- filterHits(fCs, lengths = c(27, 28), frames = list(1, 0),
                       hitMean = 50, unqhitMean = 10, fS = fS)

    plotTranscript("CUFF.37930.1", coordinates = ffCs@CDS,
                   riboData = riboDat, length = 27, cap = 200)

[Package riboSeqR version 1.24.0 Index]