Usage
plotbary(lst, coordi=1,
plot=TRUE, data=FALSE, crit=NULL,orderrule="distcenter",
modelabel=FALSE, ptext=0, leimat=NULL, symbo=NULL,
info=NULL, infolift=0, infopos=0,
xmarginleft=0, xmarginright=0, ymargin=0,
xlim=NULL, ylim=NULL, xaxt="s", yaxt="s",
nodesymbo=20, col=NULL, col.axis="black", collines=NULL, paletti=NULL,
shift=0, shiftindex=NULL,
modlabret=FALSE, modecolo=NULL, modepointer=NULL, colometh = "lst",
colothre = min(lst$level), lines=TRUE, wedge=FALSE, lty.wedge=2, title=TRUE,
titletext="coordinate", cex=NULL, nodemag=NULL, cex.sub=1, cex.axis = 1,
newtitle = FALSE, cex.lab = 1, lowest="dens", subtitle=NULL)
Arguments
lst
level set tree or shape tree; list of vectors.
The list contains at least vectors "level", "volume", and "parent".
For example, function "leafsfirst" gives a level set tree or a shape tree
as an output.
Functions "profkern" and "profhist" give a level
set tree as an output.
coordi
integer 1,...,d, when the function is d-dimensional;
gives the coordinate direction
with respect which the plot will be made.
plot
T or F; TRUE if we make a plot, otherwise FALSE.
data
T or F; TRUE if we want the output to contain some
information, for example the ordering for siblings.
This option is needed only by other plotting
functions of the package, it is not needed by the end user.
crit
d-vector of real numbers; gives a way to control
an ordering of siblings. The leftmost sibling is the one whose
barycenter is furthest away from vector "crit", in the Euclidean metric.
orderrule
lower level parameter
modelabel
T or F; TRUE if the modes will be labelled.
The default is to use labels M1, M2,...
ptext
non-negative real number; amount by which the mode
labels will be lifted.
leimat
vector of characters; the length of the vector should be
equal to the number of modes of the estimate.
This option is for the case we do not want the ordering of the
labels to be done automatically.
symbo
character; for example "L". The default value for the
automatic labelling of the modes is to use M1, M2,...
With "symbo" we may switch to L1, L2,..., for example.
info
vector of numbers or characters, whose length is equal
to the number of nodes of the level set tree.
The elements of "info" will be placed on the right side of the
nodes. For example "info" may be generated by "excmas" or we may define
"info" to contain the frequencies of the nodes.
(Frequencies may be obtained directly from the function "profhist")
infolift
real number; controls the vertical positioning of
the elements of "info".
infopos
real number; controls the horizontal positioning of
the elements of "info". Negative "infopos" will move elements of
"info" to the right hand side.
xmarginleft
non-negative real number; adds more margin on the
left hand side. The box around the plot will be moved to the left
with the amount "xmarginleft".
xmarginright
non-negative real number; adds more margin on the
right hand side. The box around the plot will be moved to the right
with the amount "xmarginright".
ymargin
nonnegative real number; adds more margin on the
top of the plot. The box around plot will be moved up
with the amount "ymargin".
xlim
vector of 2 real numbers; gives the limits for the scale
of x-axis.
ylim
vector of 2 real numbers; gives the limits for the scale
of y-axis.
xaxt
a character which specifies the x axis type; either "s" or "n";
see "par"
yaxt
a character which specifies the y axis type; either "s" or "n";
see "par"
nodesymbo
symbol for the nodes of the tree; integer 19-25;
see help(points) for the definitions
col
colour for the nodes; for example "black" or "blue".
col.axis
colour for the x and y-axis; for example "black" or
"blue".
collines
colour for lines joining nodes;
for example "black" or "blue".
paletti
a character vector of color names, in the order they will be
used to color the nodes and the lines connecting the nodes; coloring starts
from the leafs nodes and the color is changed always when two branches
are joining
shift
a real number; the amount to shift a label of a leaf node;
used to enhance the plot, see the parameter "shiftindex"
shiftindex
the index to be shifted, see the parameter "shift"
modlabret
T or F; T if the locations of the modes will be returned
modecolo
lowel level parameter
modepointer
lowel level parameter
colometh
if colometh=="lst", then colors are first chosen for
the leafs, otherwise the colors are first chosen for the roots;
for the level set trees it is better to choose "lst", but for dendrograms it
is better to color the roots first
colothre
positive real number; fixes the colors at the level given by
"colothre", this option is used for dendrograms
lines
TRUE or FALSE; used in a tail tree plot; FALSE suppresses the
parent-child lines and one can avoid over plotting
wedge
TRUE or FALSE; used in a tail tree plot if TRUE, then the
outer limts for the points will be plotted; these outer limits have a
wedge form
lty.wedge
"lty" parameter (line type) for the wedge lines
title
if TRUE, then the subtitle "coordinate i" is printed
when the coordinate is i and the the titletext is "coordinate"
titletext
character string; the text in the title will be titletext i,
if the barycenter plot is for the i:th coordinate
cex
magnification factor for the symbols; see "par"
nodemag
magnification factor for the the points
cex.sub
magnification factor for the subtitle; see "par"
cex.axis
the magnification to be used for axis annotation; see "par"
newtitle
FALSE or TRUE; if TITLE=FALSE, we can put newtitle=TRUE
to print the title as an x-axis annotation, and not as a subtitle
cex.lab
the magnification to be used for x and y labels; see "par"
lowest
"dens" or "regr"; if lowest="dens", then it is assumed that the
underlying function is a density function; if lowest="regr", then it is
assumed that the underlying function is an arbitrary multivariate real
function
subtitle
NULL or a character string; gives the subtitle of the plot