R: Plotting Routines for Multidimensional Fuzzy Set Ordinations
plot.mfso
R Documentation
Plotting Routines for Multidimensional Fuzzy Set Ordinations
Description
A set of routines for plotting, identifying, or
highlighting points in a multidimensional fuzzy set ordination (MFSO).
Usage
## S3 method for class 'mfso'
plot(x, dis=NULL, pch=1, ax=NULL, ay=NULL, ...)
## S3 method for class 'mfso'
points(x, overlay, col=2, pch=1, ...)
## S3 method for class 'mfso'
plotid(ord, dis=NULL, labels=NULL, ...)
## S3 method for class 'mfso'
hilight(ord, overlay, cols = c(2, 3, 4, 5,
6, 7), symbol = c(1, 3, 5), ...)
## S3 method for class 'mfso'
chullord(ord, overlay, cols = c(2, 3, 4, 5,
6, 7), ltys = c(1, 2, 3), ...)
## S3 method for class 'mfso'
boxplot(x, ...)
## S3 method for class 'mfso'
thull(ord,var,grain,ax=1,ay=2,col=2,grid=50,
nlevels=5,levels=NULL,lty=1,numitr=100,...)
rgl.mfso(mfso,first=1,second=2,third=3,radius=0.0005,col=0,...)
Arguments
x
an object of class ‘mfso’
ax
X axis number
ay
Y axis number
ord
an object of class ‘mfso’
mfso
an object of class ‘mfso’
dis
an object of class ‘dist’ from dist,
dsvdis, or
vegdist
overlay
a logical vector of the same length as the number of
points in the plot
labels
a vector of labels to print next to the identified points
symbol
an integer or vector of integers to control which symbols
are printed in which order on the plot by specifying values to
pch
ltys
an integer or vector of integers to control the line styles
of convex hull polygons
pch
the symbol to plot
col
the color to use for plotted symbols
cols
an integer vector for color order
var
a variable to fit with a tensioned hull
grain
the size of the moving window used to calculate the
tensioned hull
grid
the number of cells in the image version of the tensioned hull
nlevels
the number of contour levels to plot the tensioned hull
levels
a logical variable to control plotting the contours on the
tensioned hull
lty
the line type to use in drawing the contours
numitr
the number of random iterations to use to compute the
probability of obtaining as small a tensioned hull as observed
first
the X axis in the 3-D rgl plot
second
the Y axis in the 3-D rgl plot
third
the Z axis in the 3-D rgl plot
radius
the radius of the spheres used to represent points in the rgl plot
...
arguments to pass to function points
Details
Multidimensional fuzzy set ordinations (MFSO) are almost inherently graphical,
and routines to facilitate plotting and overlaying are essential to work
effectively with them.
A multidimensional fuzzy set ordination object (an object of class
‘mfso’) generally contains at least two axes, and may contain many more.
By default, the plot routine plots all possible axis pairs in order.
If ‘ax’ and ‘ay’ are specified only a single plot is produced
with X axis ax and Y axis ay. If
‘dist’ object is passed with the ‘dis=’ argument, the final panel
is a plot of the dissimilarity or distance matrix values on the X axis and the
pair-wise ordination distances on the Y axis with the correlation coefficient in
the upper left hand corner.
The ‘points’ function can be used to highlight or identify specific
points in the plot. The ‘points’ function requires a logical vector
(TRUE/FALSE) of the same length as the number of points in the plot. The
default behavior is to color the points with a respective TRUE value red. It is
possible to control the color (with col=), size (with cex=) and symbol (with
pch=) of the points.
The ‘plotid’ function can be used to label or identify specific points
with the mouse. Clicking the left mouse button adjacent to a point causes
the point to be labeled,
offset in the direction of the click relative to the point. Clicking the right
mouse button exits the routine. The default
(labels=NULL) is to label points with the row number in the data.frame (or
position in the vector) for the point. Alternatively, specifying a vector of
labels (labels=) prints the respective labels. If the data were derived from a
data.frame, the row.names of the data.frame are often a good choice, but the
labels can also be used with a factor vector to identify the distribution of
values of a factor in the ordination (but see hilight as well).
The ‘hilight’ function identifies the factor values of points in the
ordination, using color and symbols to identify unique values (up to 18 values by
default). The colors and symbols used can be specified by the ‘col=’ and
‘symbol=’ arguments, which should both be integers or integer vectors.
The default of colors 2, 3, 4, 5, 6, 7 and symbols 1, 3, 5 shows well in most
cases, but on colored backgrounds you may need to adjust ‘col=’. If you
have a factor with more than 18 classes you will need to augment the
‘symbol=’ vector with more values.
The ‘chullord’ function plots convex hulls around all points sharing the
same value for a factor variable, and colors all points of that value to match.
The convention on colors follows
hilight.
The ‘boxplot’ function plots boxplots of the μ membership values
in the MFSO.
The ‘thull’ funntion drapes a tensioned hull for variable ‘var’
over the plotted mfso.
Value
none
Note
The plotting and highlighting routines for mfso are designed to match the
same routines for other ordinations in package labdsv.
require(labdsv) # to obtain access to data sets and dissimilarity function
data(bryceveg) # vegetation data
data(brycesite) # environmental data
dis.bc <- dsvdis(bryceveg,'bray/curtis') # produce sQuote{dist} object
demo.mfso <- mfso(~elev+slope+av,dis.bc,data=brycesite)
plot(demo.mfso)
## Not run: hilight(demo.mfso,brycesite$quad) # requires interaction