plotGenome {segmentSeq} | R Documentation |
Plots the data from an alignmentData
object for a given set of
samples. Can optionally include in the plot the annotation data from a
lociData
object containing segment information.
plotGenome(aD, loci, chr = 1, limits = c(0, 1e4), samples = NULL, plotType = "pileup", plotDuplicated = FALSE, density = 0, showNumber = TRUE, logScale = FALSE, cap = Inf, ...)
aD |
An |
loci |
A |
chr |
The name of the chromosome to be plotted. Should correspond to a
chromosome name in the |
limits |
The start and end point of the region to be plotted. |
samples |
The sample numbers of the samples to be plotted. If NULL, plots all samples. |
plotType |
The manner in which the plot is created. Currently only
|
plotDuplicated |
If TRUE, then any duplicated sequence tags (i.e., sequence tags that match to multiple places in the genome) in the ‘aD’ object will be plotted on a negative scale for each sample. Defaults to FALSE (recommended). |
density |
The density of the shading lines to be used in plotting each segment. |
showNumber |
Should the row number of each segment be shown? |
logScale |
Should a log scale be used for the number of sequence tags found at each base? |
cap |
A numeric value defining a cap on the maximum number of reads to be plotted at any one point. Useful if a large number of reads at one location prevent a clear signal being seen elsewhere. |
... |
Any additional graphical parameters for passing to |
Plotting function.
Thomas J. Hardcastle
alignmentData
, heuristicSeg
, classifySeg
# Define the files containing sample information. datadir <- system.file("extdata", package = "segmentSeq") libfiles <- c("SL9.txt", "SL10.txt", "SL26.txt", "SL32.txt") # Establish the library names and replicate structure. libnames <- c("SL9", "SL10", "SL26", "SL32") replicates <- c(1,1,2,2) # Process the files to produce an `alignmentData' object. alignData <- readGeneric(file = libfiles, dir = datadir, replicates = replicates, libnames = libnames, gap = 100) # Plot the alignments to the genome on chromosome 1 between bases 1 and 10000 plotGenome(alignData, chr = ">Chr1", limits = c(1, 1e5))