humarray (version 1.0.0)

plotRanges: Plot the locations specified in a GRanges or RangedData object

Description

GRanges and RangedData objects are used in bioconductor to store genomic locations and ranges, such as transcripts, genes, CNVs and SNPs. This function allows simple plotting of this data directly from the ranged object. SNPs will be plotted as dots and ranges as lines. Either can be plotted using vertical bars at the start/end of each range. There are options for labelling and other graphical parameters. This package also creates a generic 'plot' method for GRanges and RangedData that calls this function.

Usage

plotRanges(ranged, labels = NULL, do.labs = T, skip.plot.new = F, lty = "solid", alt.y = NULL, v.lines = FALSE, ylim = NULL, xlim = NULL, scl = c("b", "Kb", "Mb", "Gb"), col = NULL, srt = 0, pos = 4, pch = 1, lwd = 1, cex = 1, ...)

Arguments

ranged

GRanges or RangedData object with genomic ranges. Should only contain one chromosome, but if not, the first will be used

labels

by default labels for each range are taken from the rownames of 'ranged', but if you want to use another column in the ranged object, specify the column name or number to use to label these ranges on the plot. Or else input a character vector the same length as ranged for custom labels.

do.labs

logical, whether or not to display these labels

skip.plot.new

logical, whether to append to an existing plot (TRUE), or start a new plot (FALSE --> default)

lty

line type to use, see '?lines()' - not used for SNP data when v.lines=FALSE

alt.y

alternative y-axis values (other than the default ordering from the input) This can be a vector of length 1 or length(ranged), or else a column name in ranged to take the values from

v.lines

TRUE will plot the ranges as pairs of vertical lines, occupying the full vertical extent of the plot, whereas FALSE will plot the ranges as individual horizontal lines

ylim

numeric, length 2, the y-axis limits for the plot, same a 'ylim' for ?plot()

xlim

numeric, length 2, the x-axis limits for the plot, same a 'xlim' for ?plot(), This shouldn't usually be needed as the automatic x-limits should work well, however is here in case fine tuning is required.

scl

character, the scale that the x axis uses, ie, 'b','kb','mb', or 'gb', meaning base-pairs, kilobases, megabases or gigabase-pairs.

col

character, colour, same as 'col' argument for plot(), etc.

srt

integer, text rotation in degrees (see par) for labels

pos

integer, values of '1', '2', '3' and '4', respectively indicate positions below, to the left of, above and to the right of the specified coordinates. See 'pos' in graphics:text()

pch

point type, see '?points()' - not used for ranged data

lwd

line width, see '?lines()' - not used for SNP data when v.lines=FALSE

cex

font/symbol size, see '?plot()' - passed to plot, points if using SNP data

...

further arguments to 'plot', so long as skip.plot.new==FALSE.

Value

Plots the ranges specified in 'ranged' to the current plot, or to a new plot

Examples

require(GenomicRanges)
rr <- in.window(rranges(5000),chr=6,pos=c(28,32),unit="mb") # make some random MHC ranges
rownames(rr) <- paste0("range",1:length(rr))
# plotRanges vertically 
#print(rr)
plotRanges(rr,v.lines=TRUE)
# make some labels and plot as horizontal lines #
rr2 <- rr[1:5,]; mcols(rr2)[["GENE"]] <- c("CTLA9","HLA-Z","BS-1","FAKr","teST")
plotRanges(rr2,label="GENE",scl="Mb",col="black",
            xlab="Chr6 position (megabases)",
            yaxt="n",ylab="",bty="n")
# create some SNPs and plot
rr3 <- rr; end(rr3) <- start(rr3) 
rownames(rr3) <- paste0("rs",sample(10^6,nrow(rr3)))
plotRanges(rr3,col="blue",yaxt="n",ylab="",bty="n")