plotTranscript {riboSeqR} | R Documentation |
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.
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 |
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 |
... |
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)