plotCDS {riboSeqR} | R Documentation

## Plots average ribosome footprint alignment to coding sequences at 5' and 3' ends.

### Description

For each sample, the average (normalised by translation abundance over transcript) of the ribosome footprints of a given length alignments at the 5' and 3' ends of all specified transcripts beginning at each base relative to coding start/end are plotted. The bases are colour coded relative to start codon.

### Usage

    plotCDS(coordinates, riboDat, lengths = 27, min5p = -20, max5p = 200,
    min3p = -200, max3p = 20, cap, main = "", plot = TRUE, ...)

### Arguments

`coordinates` | Coordinates (as a `GRanges` object) of the coding sequences.
`riboDat` | `riboData` object containing ribosome footprint data.
`lengths` | Lengths of footprints to be plotted. May be given as a vector, in which case multiple plots will be produced.
`min5p` | The distance upstream of the translation start to be plotted.
`max5p` | The distance downstream of the translation start to be plotted.
`min3p` | The distance upstream of the translation end to be plotted.
`max3p` | The distance downstream of the translation end to be plotted.
`cap` | If given, caps the height of plotted values.
`main` | Title of the plot.
`plot` | Should the acquired matrix of mean expression be plotted? Defaults to TRUE.
`...` | Additional arguments to be passed to 'plot' and 'axes'.

### Value

Invisibly returns lists of lists of matrices containing weighted averages plotted for each sample/length combination.

### 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(0, 2),
                       hitMean = 50, unqhitMean = 10, fS = fS)

    plotCDS(coordinates = ffCs@CDS, riboDat = riboDat, lengths = 27)

[Package riboSeqR version 1.28.0 Index]