plot.nmds {labdsv} | R Documentation |
A set of routines for plotting, highlighting points, or adding fitted surfaces to NMDSs.
## 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, overlay, ax = 1, ay = 2, cols=c(2,3,4,5,6,7), glyph=c(1,3,5), origpch = 1, blank = '#FFFFFF', ...) ## S3 method for class 'nmds': chullord(ord, overlay, ax = 1, ay = 2, cols=c(2,3,4,5,6,7), ltys = c(1,2,3), ...) ## 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, ...)
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’ |
overlay |
a factor or integer vector to hilight or distinguish |
cols |
the sequence of color indices to be used |
glyph |
the sequence of glyphs (pch) to be used |
origpch |
the pch number of the glyph employed in the original plot (to be obliterated by blank) |
blank |
the color to use to erase the glyphs of the original plot |
ltys |
the sequence of line types to be used |
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 |
Function ‘plot’ produces a scatter plot 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 NMDS, 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 factor values by color and glyph.
Function ‘chullord’ is passed a factor vector or integer vector, and plots a convex hull around all points in each factor class. By specifying values for arguments ‘cols’ and ‘ltys’ it is possible to control the sequence of colors and linetypes of the convex hulls.
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 ‘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.
Function ‘plotid’ returns a vector of row numbers of identified plots
David W. Roberts droberts@montana.edu http://ecology.msu.montana.edu/droberts
http://ecology..msu.montana.edu/labdsv/R
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))