plot.stamFit {stam}R Documentation

Plots for StAM Model Fit


Overall alpha vs. delta plot as well as nodewise scatter plots on performance/redundancy and specificity/sensitivity.


plot.stamFit(x, outfile = NULL, aclass = NULL, main = NULL,
             which = 0, res = 72, ps = FALSE, pointsize = 12, ...)


x the object of type stamFit for which the plots are to be drawn
outfile name of output file if postscript or PNG graphics is to be generated. The extension of the file is chosen automatically according to the ps argument. The filename is also augmented by suffixses to distinguish the plots generated. If no outfile is specified, an interactive plot is attempted
aclass the name of the phenotype class of interest, usually the disease class
which choose the plot to be generated. 1:alpha vs. delta, 2:nodewise evaluation, 0:both plots in interactive mode, non otherwise.
main the main title of the plot, generated automatically if left blank
res resolution in points per inch
ps if set to TRUE postscript output is generated
pointsize the standard fontsize
... additional arguments to be passed to plot


If several values for alpha are provided to plot.stamFit generates a compound score vs. shrinkage level plot. For each alpha one line is drawn and the best shrinkage (where the minimum is achieved) is marked. In a second pane of the same plot alpha is plotted vs. these best shrinkage levels.

Additionally nodewise scatter plots comparing performance vs. redundancy and sensitivity vs. specificity are generated.


Claudio Lottaz

See Also

[Package stam version 1.0.3 Index]