Usage
oncotree.fit(dataset, error.fun = function(x, y){sum((x - y)^2)})
## S3 method for class 'oncotree':
print(x, \dots)
## S3 method for class 'oncotree':
plot(x, edge.weights = c("none", "observed", "estimated"),
edge.digits=2, node.coords=NULL, plot=TRUE, cex = par("cex"),
col.edge=par("col"), col.text=par("col"), col.weight=par("col"),...)
pstree.oncotree(x, edge.weights=c("none","observed","estimated"), edge.digits=2,
shape=c("none","oval", "circle", "triangle", "diamond"),
pstree.options=list(arrows="->", treefit="loose", arrowscale="1.5 0.8", nodesep="3pt"))Arguments
dataset
A data frame or a matrix with variable names as
a listing of genetic events taking on binary values indicating
missing (0) or present (1). Each row is an independent sample.
error.fun
A function of two variables that measures the
deviation of the observed marginal frequencies of the events
(which will be the first argument in the call) from the estimated ones.
The false positive and negative error rates are obtained by min
x
An object of class oncotree.
edge.weights
Choice of edge weights to show on the plot.
edge.digits
The number of significant digits to use when displaying edge weights.
node.coords
A matrix with node-coordinates or NULL if the coordinates should be
computed automatically (default).
plot
Logical; indicates whether the tree should be plotted.
cex
Scaling factor for the text in the nodes.
col.edge
color of the tree edges.
col.text
color of the node label.
col.weight
color of the edge weights.
...
Ignored for print. For plot these can
be graphical parameters passed to lines when the edges are
drawn
shape
The shape of the node in the pst-tree representation.
pstree.options
Additional options for pst-tree. See the pstricks
documentation for possible values.