- tree
an object of class "phylo"
.
- x
vector of trait values; or a matrix. If x
is a vector it must have names that correspond to the tip labels of tree
. If x
is a matrix (and it probably should be a matrix, not a data frame) then the row names of the matrix should correspond to the tip labels of the phylogeny. In the case of dot.legend
, the x coordinate of the legend.
- legend
logical value indicating whether or not a legend should be plotted.
- method
tree plotting method to be used internally. Will switch to method="phylogram"
if the number of traits is greater than one. For dot.legend
, it should be the method that was used for the plot.
- standardize
a logical value indicating whether or not to standardize x
, or each column of x
, to have a mean of zero & variance of one prior to analysis.
- y
y coordinate of the legend.
- min
minimum value for dot.legend
.
- max
maximum value for dot.legend
.
- Ntip
number of tips in the plotted tree for dot.legend
.
- length
length of legend.
- prompt
logical value indicating whether or not to prompt for legend position.
- ...
optional arguments. In the case of dotTree
, these will be passed to plotTree
or a different internally used plotting function for method="phylogram"
. See phylo.heatmap
for more detail on these arguments. Other option for dotTree
also include data.type
("continuous"
or "discrete"
), colors
, length
, for data type "continuous"
the length of the legend in terms of plotted circles, x.space
, the spacing of the columns in the plotted data matrix, and leg.space
, the spacing of the legend dots (again, for data.type="continuous"
only).