Plots histograms 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 |
NGROUPS = scalar |
Number of groups into which to classify the DATA units; default 100 |
COLOUR = text or scalar |
Colour to use for the bars of the histogram; default 'red' |
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 |
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 or single plots when the DATA variate contains data from more than one slide (single, 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 * |
YMINIMUM = scalar |
Minimum value on the y-axis of the histogram |
YMAXIMUM = scalar |
Maximum value on the y-axis of the histogram |
XMINIMUM = scalar |
Minimum value on the x-axis of the histogram |
XMAXIMUM = scalar |
Maximum value on the x-axis of the histogram |
Parameter
DATA = variates or pointers |
Data values to plot |
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Description
The data values are supplied 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 histogram 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 NGROUPS option defines the number of groups into which to classify the DATA variate, i.e. the number of bars in each histogram (default 100). The COLOUR option defines the colour to use for the bars. You can set option TRANSFORMATION=log2 to transform the DATA values to logarithms base 2 before plotting. The ARRANGEMENT option controls whether the histograms for the slides are plotted singly, in separate frames, or together in a trellis arrangement (the default) when the DATA variate contains data from more than one slide. The SCALING option controls whether a common scale is used for the single plots, while the NROWS and NCOLUMNS options specify the numbers of rows and columns on the page in a trellis plot.
The TITLE, YTITLE and XTITLE options can supply titles for the graphs, the y-axes and the x-axes, 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. The YMAXIMUM, YMAXIMUM, XMINIMUM and XMAXIMUM options can be used to set the lower and upper limits on the y and x-axes of the histograms.
Options: SLIDES, SLIST, NGROUPS, COLOUR, TRANSFORMATION, SCALING, NROWS, NCOLUMNS, TITLE, YTITLE, XTITLE, ARRANGEMENT, WINDOW, DEVICE, GRAPHICSFILE, YMAXIMUM, YMAXIMUM, XMINIMUM, XMAXIMUM.
Parameter: DATA.
Action with RESTRICT
MAHISTOGRAM takes account of any restrictions on DATA or SLIDES.
See also
Procedures: DMADENSITY, FDRBONFERRONI, FDRMIXTURE, MACALCULATE, MAESTIMATE, MAPCLUSTER, MAPLOT, MASCLUSTER, MASHADE, MAVOLCANO, MA2CLUSTER, MNORMALIZE.
Commands for: Microarray data.
Example
CAPTION 'MAHISTOGRAM 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'
" Trellis Plot of Histograms of logged Red & Green Foreground values."
MAHISTOGRAM [NGROUPS=100; TRANSFORMATION=log2; SLIDES=Slide;\
NROWS=2; NCOLUMNS=2; DEVICE=1; COLOUR=2; WINDOW=3] F1_Mean
MAHISTOGRAM [NGROUPS=100; TRANSFORMATION=log2; SLIDES=Slide;\
NROWS=2; NCOLUMNS=2; DEVICE=1; COLOUR=3; WINDOW=3] F2_Mean
" Single page per histogram, for just first two slides of logRatio."
MAHISTOGRAM [NGROUPS=100; TRANSFORMATION=none; SLIDES=Slide;\
SLIST=!(1,2); ARRANGEMENT=single; SCALING=common] logRatio
ELSE
CAPTION 'Microarray example datasets have not been installed.'
ENDIF