Produces shade plots to display spatial variation of microarray data (D.B. Baird).
Options
SLIDES = factor or text |
Defines the slides when the DATA variate contains data from more than one slide |
|---|---|
SLIST = variate or text |
Subset of slides to plot; default * i.e. all |
ROWS = factor or variate |
Row to which each DATA unit belongs |
COLUMNS = factor or variate |
Column to which each DATA unit belongs |
COLOURS = text, scalar or variate |
Colours to use for the plots; default !t(blue,red) |
SHADING = string token |
Shading scale (natural, percentiles); default natu |
TITLE = text |
Title for the graph |
YTITLE = text |
Title for the y-axis |
XTITLE = text |
Title for the x-axis |
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 * |
Parameter
DATA = variates or pointers |
Values for each shade plot |
|---|
Description
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 ROWS and COLUMNS parameters supply a factor or variate, to define the row and column positions within each slide.
The 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).
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, ROWS, COLUMNS, COLOURS, SHADING, TITLE, YTITLE, XTITLE, WINDOW, DEVICE, GRAPHICSFILE.
Parameter: DATA.
Action with RESTRICT
Restrictions are ignored.
See also
Procedures: DMADENSITY, FDRBONFERRONI, FDRMIXTURE, MACALCULATE, MAESTIMATE, MAHISTOGRAM, MAPCLUSTER, MAPLOT, MASCLUSTER, MAVOLCANO, MA2CLUSTER, MNORMALIZE.
Commands for: Microarray data.
Example
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