codelink (version 1.40.2)

plotMA: MA plot

Description

Takes a Codelink object and plot M vs A.

Usage

plotMA(object, array1 = 1, array2 = NULL, cutoff = c(-1, 1), label = NULL, type = NULL, high.list = NULL, high.col = "blue", high.pch = 21,
	high.bg = "cyan",	snr = NULL, snr.cutoff = 1, legend.x = NULL, pch = ".", 
	subset = NULL, title = NULL, xlim = NULL, ylim = NULL)

Arguments

object

an object of class "Codelink" or "MAarrayLM".

array1

first array to be used.

array2

second array to be used.

cutoff

cutoff to be used as fold change markeer.

label

type of labeling used in legend.

type

spot type information.

high.list

list of genes highlighted.

high.col

color used for high genes.

high.pch

pch used for high genes.

high.bg

background color used for high genes.

snr

vector with SNR values, usually, taking rowMeans() from a SNR matrix.

snr.cutoff

SNR cutoff used for label spots.

legend.x

relative position of the legend.

pch

pch style used to main spots.

subset

subset of spots used to plot based on 'type' slot.

title

title of the plot.

xlim

range for the X axis.

ylim

range for the Y axis.

Details

This function has suffered recent re-working, to increase the usability and to clean a little bit the code.

If array2 is NULL a median array is computed using all available arrays. Then the values of M and A are computed using the following formula:

M = array2 - array1

A = (array2 + array1) / 2

If type information is available in the Codelink object, or provided throught the 'type' argument, spots are colored based on that. DISCOVERY spots are plotted black with pch = "." whereas the other classes are plotted with different background colors, using gray as border to increase contrasts. For that pch = 21 is used. If snr is specified as label option, the SNR is used to label spots, if available in the Codelink object. In this case, the mean SNR across all arrays is used when array2 = NULL.

Some parameters may not be working right now, as the new function is using a different method to labels spots.

The legend is 'automagically' located, but this can be overrided with the legend.x argument.

In addition, a subset of the spots can be plotted based on type information when available. This allows, for example, to plot only DISCOVERY spots.

Examples

## Not run: 
#     data(codelink.example)
#     plotMA(codelink.example)
# ## End(Not run)