plot.nmds {labdsv}R Documentation

Plotting Routines For Nonmetric Multi-dimensional Scaling Ordinations

Description

A set of routines for plotting, highlighting points, or adding fitted surfaces to NMDSs.

Usage

## S3 method for class 'nmds':
plot(x, ax = 1, ay = 2, col = 1, title = "", pch = 1, ...)
## S3 method for class 'nmds':
points(x, which, ax = 1, ay = 2, col = 2, pch = 1, cex = 1, ...)
## S3 method for class 'nmds':
plotid(ord, ids = seq(1:nrow(ord$points)), ax = 1, ay = 2, 
    col = 1, ...)
## S3 method for class 'nmds':
hilight(ord, factor, ax = 1, ay = 2, ...)
## S3 method for class 'nmds':
surf(ord, var, ax = 1, ay = 2, col = 2, labcex = 0.8, 
    family = gaussian, ...)
## S3 method for class 'nmds':
jsurf(ord, var, ax = 1, ay = 2, col = 2, labcex = 0.8, 
    family = gaussian, ...)

Arguments

x an object of class ‘nmds’
ax the dimension to use for the X axis
ay the dimension to use for the Y axis
title a title for the plot
which a logical variable to specify points to be highlighted
ord an object of class ‘nmds’
factor a factor or integer vector
var a variable to be surfaced
family controls the link function passed to ‘gam’: one of ‘gaussian’, ‘binomial’, or ‘poisson’
ids identifier labels for samples. Defaults to 1:n
col color index for points or contours
labcex size of contour interval labels
pch plot character: glyph to plot
cex character expansion factor: size of plotted characters
... arguments to pass to the plot function

Details

Function ‘plot’ produces a scatterplot of sample scores for the specified axes, erasing or over-plotting on the current graphic device. Axes dimensions are controlled to produce a graph with the correct aspect ratio. Functions ‘points’, ‘plotid’, ‘surf’, and ‘jsurf’ add detail to an existing plot. The axes specified must match the underlying plot exactly.

Function ‘plotid’ identifies and labels samples (optionally with values from a third vector) in the PCO, and requires interaction with the mouse: left button identifies, right button exits.

Function ‘points’ is passed a logical vector to identify a set of samples by color of glyph. It can be used to identify a single set meeting almost any criterion that can be stated as a logical expression.

Function ‘hilight’ is passed a factor vector or integer vector, and identifies identifies factor values by color and glyph.

Functions ‘surf’ and ‘jsurf’ calculate and plot fitted surfaces for logical or quantitative variables; ‘jsurf’ jitters the coordinates to avoid problems with identical values in fitting the surface. The functions are simply wrappers for the gam function, and send the sample coordinates and the ‘var’ variable to ‘gam’ to model. The coordinates and the fitted values from ‘gam’ are then passed to interp, which plots the contours. The default link function for fitting the GAMs is sQuote{gaussian}, suitable for unbounded continuous variables. For logical variables you should specify ‘family = binomial’ to get a logistic GAM, and for integer counts you should specify ‘family = poisson’ to get a Poisson GAM.

Value

Function ‘plotid’ returns a vector of row numbers of identified plots

Author(s)

David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/labdsv

See Also

points, plotid, hilight, surf, and jsurf

Examples

data(bryceveg)
data(brycesite)
dis.bc <- dsvdis(bryceveg,'bray/curtis')
nmds.1 <- nmds(dis.bc,5)
plot(nmds.1)
points(nmds.1,brycesite$elev>8000)
surf(nmds.1,brycesite$elev)
## Not run: plotid(nmds.1,ids=row.names(bryceveg))

[Package labdsv version 1.0-1 Index]