MAPLOT procedure

Produces two-dimensional plots of microarray data (D.B. Baird).

Options

SLIDES = factor

Slide to which each DATA unit belongs

SLIST = variate or text

Subset of slides to plot; default * i.e. all

GROUPS = factor

Specifies groups within slides

COLOURS = scalar or variate

Colours to use for the plots

SYMBOLS = scalar or variate

Symbols to use for the plots

REFERENCELINE = string

Reference line to include (identity, zero, none); default none

TRANSFORMATION = string

Whether to transform data to logarithms base 2 (log2, none); default none

SCALING = string

Whether to use a common scale when not using Trellis plots (common, none); default comm

BANDS = string

Whether to plot approximate confidence bands (confidence, none); default none

SMOOTHEDMEAN = string

Whether to plot spline smooth of mean (yes, no); default no

NROWS = scalar

Number of rows on a page in a trellis plot

NCOLUMNS = scalar

Number of columns on a page in a trellis plot

TITLE = text

Title for the graph

YTITLE = text

Title for the y-axis

XTITLE = text

Title for the x-axis

ARRANGEMENT = string

Whether to use trellis, single or multiple plots (separate, overlaid, trellis); default trel

WINDOW = scalar

Window number for the graphs; default 3

DEVICE = scalar

Device number on which to plot the graphs

GRAPHICSFILE = text

What graphics filename template to use to save the graphs; default *

Parameters

Y = variates

Y-coordinates

X = variates

X-coordinates

Description

MAPLOT produces two-dimensional plots of microarray data or transformed data using log base 2. The x- and y-coordinates are supplied, in variates, using the X and Y parameters, respectively. The SLIDES option supplies a factor to define the slides. By default a graph is produced for the data from every one of the slides, but you can set option SLIST to a variate or text to define a subset of the slides to plot.

The REFERENCELINE option allows you to include either an identity reference line or a horizontal reference at zero. The BANDS option includes approximate confidence bands, and the SMOOTHEDMEAN option adds a spline smooth of the mean. By default none of these are plotted.

The COLOURS and SYMBOLS options can be each be set to a scalar or a variate to define the colour(s) and symbol(s), respectively, to use for the plots. The TITLE, YTITLE and XTITLE options can supply titles for the graph, the y-axis and the x-axis, respectively. The WINDOW option specifies the window to use (by default 3), and the KEYWINDOW option can specify a window for a key (by default there is none). You can use the DEVICE option to plot to a device other than the screen. The GRAPHICSFILE option specifies then supplies a template for the file names.

Options: SLIDES, SLIST, GROUPS, COLOUR, SYMBOLS, REFERENCELINE, TRANSFORMATION, SCALING, NROWS, NCOLUMNS, TITLE, YTITLE, XTITLE, ARRANGEMENT, WINDOW, DEVICE, GRAPHICSFILE.

Parameters: Y, X.

Action with RESTRICT

MAPLOT takes account of any restrictions on X, Y or SLIDES.