Produces volcano plots of microarray data (D.B. Baird).
Options
NGROUPS = scalar |
Number of groupings for a Z variate; default 10 |
|---|---|
COLOURS = text, scalar or variate |
Colours to use for the plots; default !t(blue,red) |
SYMBOL = scalar |
Symbol to use for the points; default 1 |
TRANSFORMATION = string token |
Whether to transform data to logarithms base 2 (log10, none); default log10 |
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 |
KEYWINDOW = scalar |
Window number for the graphs; 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
X = variates |
X-coordinates |
|---|---|
Y = variates or factors |
Y-coordinates |
Z = variates or factors |
Z-coordinates |
Description
MAVOLCANO produces volcano plots of microarray data. The y-coordinates are specified by the Y parameter. Typically these are probabilities, in which case they are usually transformed to -log10(Y). This transformation is thus applied by default, but you can set option TRANSFORMATION=none to suppress it. Less commonly the y-coordinates may be t-values. The x-coordinates are specified by the X parameter. These are usually measures of differential expression such as log-ratios.
The Z parameter can specify a variate or factor to use to colour the points on the graph. If this is a variate, the values are grouped into the number of percentiles specified by the NGROUPS option. The COLOURS option supplies a text, scalar or variate to define the colours to use for the plots. The default of !t(blue,red) uses colours ranging from blue to red. The SYMBOL option defines the symbol to use for the points (default 1).
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: NGROUPS, COLOURS, SYMBOL, TRANSFORMATION, TITLE, YTITLE, XTITLE, WINDOW, KEYWINDOW, DEVICE, GRAPHICSFILE.
Parameters: X, Y, Z.
Action with RESTRICT
MAVOLCANO takes account of any restrictions on X, Y or Z.
See also
Procedures: DPROBABILITY, FDRBONFERRONI, FDRMIXTURE.
Commands for: Microarray data, Graphics.
Example
CAPTION 'MAVOLCANO example'; STYLE=meta
ENQUIRE CHANNEL=-1; EXIST=check; NAME=\
'%GENDIR%/Data/Microarrays/ApoAIKnockOutEffects.GSH'
IF check
SPLOAD '%GENDIR%/Data/Microarrays/ApoAIKnockOutEffects.GSH'
MAVOLCANO [TRANSFORMATION=log10; NGROUPS=10;\
TITLE='APO Knock-out Mouse Expt KO vs Normal';\
YTITLE='-Log10(Probability)'; XTITLE='Knock-out log-Ratio']\
Y=PrCon[1]; X=Cont[1]; Z=Res_SD
ELSE
CAPTION 'Microarray example datasets have not been installed.'
ENDIF