plotTranscript: Plots ribosome footprint abundance and mRNA coverage (if...
In riboSeqR: Analysis of sequencing data from ribosome profiling experiments

Description Usage Arguments Details Value Author(s) Examples

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.

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

`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.

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.

NULL; plotting function.

Thomas J. Hardcastle

#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)