plotPlate {prada}R Documentation

Plot a well statistic in false color representation.

Description

Plot a well statistic in false color representation. The plot is supposed to resemble the physical geometry of a microtitre plate.

Usage

plotPlate(x, nrow = 8, ncol = 12, ind = 1:(ncol*nrow), main, xrange,
          col, device, file, width, na.action = "zero",
          desc = as.character(c(NA, NA)), char)

Arguments

x Numeric vector of length ncol*nrow (except if argument ind is specified).
nrow Numeric of length 1. The number of rows of the plate.
ncol Numeric of length 1. The number of columns of the plate.
ind Optional integer vector of equal length as x. It indicates the position of the respective value of x on the plate. Can be used to adress the problem of missing values. Each well that is not allocated a value of x by ind will not be plotted.
main Character of length 1. Plot title. This arguments gets passed on to text as the argument labels.
xrange Range of x that is mapped into the color scale.
col Character vector. Usually the names of two or three colors between which the color map is interpolated, using the function colorRampPalette.
device Character. Name of a valid graphics device, e.g. x11, png, pdf.
file The file argument of the call to device, i.e. the name of the graphics output file.
width The width argument of the call to device, i.e. the width of the graphic.
na.action Character. One of "zero" "omit" or "xout". How should the wells for which x is NA be treated? For "zero", they are plotted as if the value were 0. For "omit", they are omitted. For "xout", they are crossed out.
desc Character of length 2. Legend for the two ends of the colorbar, e.g. 'act' and 'inh'.
char An optional character vector of equal length as x (except if argument ind is specified). Each element of the vector may contain one single char to be superimposed on the respective well or NA for no plotting.

Details

Argumentind allows the user to indicate the position (well number) for each element of vector x on the plate. This can be used either to change the order in which elements of x are to be plotted or to deal with the problem of missing data for some of the wells on a plate.

To further increase the amount of information of the platePlot one may decorate wells with single characters using argument char. Each element of char != NA will be superimposed on the respective well (see examples).

Value

The function produces a plot in the graphics device specified by the device argument.
It returns a list with two elements. The element which is a vector with the indices of those elements in x that were plotted (see argument na.action). The element coord is a length(which) by 4 matrix in which each row specifies the corners of a rectangle that contains a well. It is intended to be use as an argument to a subsequent call to imageMap.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber

See Also

imageMap

Examples

plotPlate(runif(96), main="example 1", col=c("#0000e0", "#e00000"), width=7, desc=c("act", "inh"))
plotPlate(runif(384), nrow=16, ncol=24, main="example 2", col=c("#0000e0", "white", "#e00000"), width=7)
plotPlate(runif(48), main="example 3", col=c("#0000e0", "#e00000"), width=7, ind=c(1:24, 73:96))
x <- runif(96)
x[sample(96, 10)] <- NA
plotPlate(x, main="example 4", col=c("#0000e0", "#e00000"), width=7, char=c(rep(NA, 72), LETTERS[1:24]), na.action="xout")

[Package prada version 1.3.1 Index]