Interactive version of genomePlot

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Description

Interactive version of genomePlot. Allows the user to click near a probe and the name of that probe will be displayed next to it.

Usage

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IDProbes(input, array = 1, naut = 22, Y = FALSE, X
                 = FALSE, status, values, pch, cex, col, chrominfo =
                 chrominfo.Mb, ylim = c(-2, 2), ylb = "Log2Ratio",
                 chrom.to.plot = 1, xlim = c(0,NA))

Arguments

input

an object of class MAList or SegList

array

integer of the array (sample) to be plotted.

naut

number of autosomes in the organism

Y

TRUE if chromosome Y is to be plotted, FALSE otherwise

X

TRUE if chromosome X is to be plotted, FALSE otherwise

status

character vector giving the control status of each spot on the array, of same length as the number of rows of log2ratios(input). If omitted, all points are plotted in the default color, symbol and size.

values

character vector giving values of status to be highlighted on the plot. Defaults to unique values of status. Ignored if there is no status vector.

pch

vector or list of plotting characters. Default to integer code 16. Ignored is there is no status vector.

col

numeric or character vector of colors, of the same length as values. Defaults to 1:length(values). Ignored if there is no status vector.

cex

numeric vector of plot symbol expansions, of the the same length as values. Defaults to 0.2 for the most common status value and 1 for the others. Ignored if there is no status vector.

chrominfo

a chromosomal information associated with the mapping of the data.

ylim

Minimum y-scale to use for plotting.

chrom.to.plot

Specify which chromosome to plot

ylb

label for the Y-axis.

xlim

limits for the x-axis

Author(s)

Mike Smith

See Also

genomePlot

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