plot.stamFit {stam} | R Documentation |
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 stam.fit 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