Produces two-dimensional plots of microarray data (D.B. Baird).
Options
SLIDES = factor or text |
Defines the slides when the X and Y variates contain data from more than one slide |
|---|---|
SLIST = variate or text |
Subset of slides to plot; default * i.e. all |
GROUPS = factor |
Specifies groups within slides |
COLOURS = text, scalar or variate |
Colours to use for the plots |
SYMBOLS = scalar or variate |
Symbols to use for the plots |
REFERENCELINECHOICE = string token |
Reference line to include (identity, zero, none); default none |
TRANSFORMATION = string token |
Whether to transform data to logarithms base 2 (log2, none); default none |
SCALING = string token |
Whether to use a common scale when not using Trellis plots (common, none); default comm |
BANDS = string token |
Whether to plot approximate confidence bands (confidence, none); default none |
SMOOTHEDMEAN = string token |
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 token |
Whether to use trellis, single or multiple plots when the X and Y variates contain data from more than one slide (separate, overlaid, trellis); default trel |
WINDOW = scalar |
Window number for the graphs; default 3 |
KEYWINDOW = scalar |
Window number for the key; default 0 |
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 or pointers |
Y-coordinates |
|---|---|
X = variates or pointers |
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 or pointers, using the X and Y parameters, respectively. If you have data from several slides, you can set DATA either to a list of variates, or to a pointer to the variates (one for each slide), or to a single variate containing the data from all the slides. When multi-slide data are in a single DATA variate, the SLIDES option must supply a factor to identify the slides. If they are in a pointer, the SLIDES option can be omitted, or it can supply a text to identify the slides. By default, a plots are produced for the data from every slide, but you can set option SLIST to a variate or text to define a subset of the slides to plot.
The REFERENCELINECHOICE 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 option can be set to a text, scalar or variate to define the colour(s) to use for the plots, and the SYMBOLS option can be set to a scalar or variate to define the symbols. 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, REFERENCELINECHOICE, TRANSFORMATION, SCALING, NROWS, NCOLUMNS, TITLE, YTITLE, XTITLE, ARRANGEMENT, WINDOW, KEYWINDOW, DEVICE, GRAPHICSFILE.
Parameters: Y, X.
Action with RESTRICT
MAPLOT takes account of any restrictions on X, Y or SLIDES.
See also
Procedures: DMADENSITY, FDRBONFERRONI, FDRMIXTURE, MACALCULATE, MAESTIMATE, MAHISTOGRAM, MAPCLUSTER, MASCLUSTER, MASHADE, MAVOLCANO, MA2CLUSTER, MNORMALIZE.
Commands for: Microarray data.
Example
CAPTION 'MAPLOT example'; STYLE=meta
ENQUIRE CHANNEL=-1; EXIST=check; NAME=\
'%GENDIR%/Data/Microarrays/Data13-6-9.gwb'
IF check
SPLOAD '%GENDIR%/Data/Microarrays/Data13-6-9.gwb'
" Plot of Red vs Green Foreground on log2 scale in trellis plot."
MAPLOT [ARRANGEMENT=trellis; SLIDES=Slide; GROUPS=Block; SYMBOL=1;\
BANDS=none; REFERENCE=identity; TRANSFORM=Log2]\
Y=F1_Mean; X=F2_Mean
" Plot of logRatio vs Intensity, one slide per plot with
approx confidence limits."
MAPLOT [ARRANGEMENT=multiple; SLIDES=Slide; SYMBOL=1; SMOOTHEDMEAN=yes;\
REFERENCE=zero; BANDS=confidence; TRANSFORM=none; WINDOW=3]\
Y=logRatio; X=Intensity
" Single overlaid Plot of logRatio vs Intensity."
MAPLOT [ARRANGEMENT=single; SLIDES=Slide; SYMBOL=1;\
REFERENCE=none; TRANSFORM=none; WINDOW=1; KEYWINDOW=2]\
Y=logRatio; X=Intensity
ELSE
CAPTION 'Microarray example datasets have not been installed.'
ENDIF