genoPlot {genoset} | R Documentation |
Plot location data and chromosome boundaries from a GenoSet or GRanges object against data from a numeric or Rle. Specifying a chromosome name and optionally a 'xlim' will zoom into one chromosome region. If more than one chromosome is present, the chromosome boundaries will be marked. Alternatively, for a numeric x and a numeric or Rle y, data in y can be plotted at genome positions x. In this case, chromosome boundaries can be taken from the argument locs. If data for y-axis comes from a Rle lines are plotted representing segments. X-axis tickmarks will be labeled with genome positions in the most appropriate units.
genoPlot(x, y, ...) ## S4 method for signature 'numeric,numeric' genoPlot(x, y, add = FALSE, xlab = "", ylab = "", col = "black", locs = NULL, ...) ## S4 method for signature 'numeric,Rle' genoPlot(x, y, add = FALSE, xlab = "", ylab = "", col = "red", locs = NULL, lwd = 2, xlim = NULL, ...) ## S4 method for signature 'GenoSetOrGenomicRanges,ANY' genoPlot(x, y, chr = NULL, add = FALSE, pch = ".", xlab = "", ylab = "", ...)
x |
GenoSet (or descendant) or GRanges |
y |
numeric or Rle |
... |
Additional plotting args |
add |
Add plot to existing plot |
xlab |
character, label for x-axis of plot |
ylab |
character, label for y-axis of plot |
col |
character, color to plot lines or points |
locs |
GRanges, like rowRanges slot of GenoSet |
lwd |
numeric, line width for segment plots from an Rle |
xlim |
integer, length two, bounds for genome positions. Used in conjunction with "chr" to subset data for plotting. |
chr |
Chromosome to plot, NULL by default for full genome |
pch |
character or numeric, printing character, see points |
TRUE
signature(x = "GenoSetOrGenomicRanges", y = "ANY")
Plot feature locations and data from one sample.
signature(x = "numeric", y = "numeric")
Plot numeric location and a vector of numeric data.
signature(x = "numeric", y = "Rle")
Plot numeric location and a vector of Rle data. Uses lines for Rle runs.
Other "genome plots": genomeAxis
data(genoset,package="genoset") genoPlot( x=genoset.ds,y=genoset.ds[,1,"lrr"] ) genoPlot( genoPos(genoset.ds), genoset.ds[,1,"lrr"], locs=rowRanges(genoset.ds) ) # The same genoPlot( 1:10, Rle(c(rep(0,5),rep(3,4),rep(1,1))) )