pamr.makeclasses
Using this function the user interactively defines a new set of classes,
to be used in pamr.train, pamr.cv etc.
After invoking pamr.makeclasses, a clustering tree is drawn.
This callss the R function hclust
, and any arguments for
hclust
can be passed to it.
Using the left button, the user clicks at the junction point defining
the subgroup 1. More groups can be added to class 1 by clicking
on further junction points. The user ends the definition of class 1 by
clicking on the rightmost button [in Windows, an additional menu appears
and he chooses Stop] . This process is continued for classes 2,3 etc.
Note that some sample may be left out of the new classes.
Two consecutive clicks of the right button ends the definition for all classes.
At the end, the clustering is redrawn, with the new class labels shown.
Note: this function is "fragile". The user must click close to the junction
point, to avoid confusion with other junction points. Classes 1,2,3..
cannot have samples in common (if they do, an Error message will appear).
If the function is confused about the desired choices, it will
complain and ask the user to rerun pamr.makeclasses. The user should
also check that the labels on the final redrawn cluster tree agrees with the desired
classes.