riboSeqR (version 1.6.0)

plotTranscript: 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 = "", ...)

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).

...

Additional arguments to be passed to plotting function.

Value

NULL; 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.

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 0-frame,
# 28-mers are principally in the 2-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)

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