Produces shade plots to display spatial variation of microarray data (D.B. Baird).
||Defines the slides when the
||Subset of slides to plot; default
||Row to which each
||Column to which each
||Colours to use for the plots; default
||Shading scale (
||Title for the graph|
||Title for the y-axis|
||Title for the x-axis|
||Window number for the graphs; default 3|
||Device number on which to plot the graphs|
||What graphics filename template to use to save the graphs; default
||Values for each shade plot|
The data values are supplied, in either one or several variates or a pointer to variates, using the
DATA parameter. 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 plot is 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
COLUMNS parameters supply a factor or variate, to define the row and column positions within each slide.
COLOURS option supplies a text, scalar or variate to define the colours to use for the plots. The default of
!(blue,red) uses colours ranging from blue to red. The
SHADING option chooses whether to allocate the
DATA values to shades by percentiles, thus giving similar amounts of each colour on the plots, or by their actual values (the default).
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.
Restrictions are ignored.
Commands for: Microarray data.
CAPTION 'MASHADE 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' " Spatial Plot of spot brightness for just first two slides." MASHADE [SLIDES=Slide; SLIST=!(1,2); ROWS=Slide_Row; COLUMNS=Slide_Column]\ Intensity " Spatial Plot of logRatio for all slides using percentile scaling." MASHADE [SLIDES=Slide; ROWS=Slide_Row; COLUMNS=Slide_Column;\ SHADING=percentile] logRatio ELSE CAPTION 'Microarray example datasets have not been installed.' ENDIF