A set of routines for plotting, highlighting points, or adding fitted surfaces to NMDSs.
# S3 method for nmds
plot(x, ax = 1, ay = 2, col = 1, title = "", pch = 1, …)
# S3 method for nmds
points(x, which, ax = 1, ay = 2, col = 2, pch = 1, cex = 1,
breaks=FALSE, …)
# S3 method for nmds
plotid(ord, ids = seq(1:nrow(ord$points)), ax = 1, ay = 2,
col = 1, …)
# S3 method for nmds
hilight(ord, overlay, ax = 1, ay = 2, title="", cols=c(2,3,4,5,6,7),
glyph=c(1,3,5), …)
# S3 method for nmds
chullord(ord, overlay, ax = 1, ay = 2, cols=c(2,3,4,5,6,7),
ltys = c(1,2,3), …)
# S3 method for nmds
surf(ord, var, ax = 1, ay = 2, thinplate = TRUE, col = 2, labcex = 0.8,
family = gaussian, gamma=1, grid=50, …)
# S3 method for nmds
thull(ord,var,grain,ax=1,ay=2,col=2,grid=50,nlevels=5,levels=NULL,lty=1,
numitr=100,…)
# S3 method for nmds
density(ord, overlay, ax = 1, ay = 2, cols = c(2, 3, 4, 5,
6, 7), ltys = c(1, 2, 3), numitr, ...)an object of class ‘nmds’
the dimension to use for the X axis
the dimension to use for the Y axis
a title for the plot
a logical variable to specify points to be highlighted
a logical switch to control using variable glyph sizes in ‘points’
an object of class ‘nmds’
a factor or integer vector to hilight or distinguish
the sequence of color indices to be used
the sequence of glyphs (pch) to be used
the sequence of line types to be used
a variable to be surfaced or tension hulled
a logical variable to control the fitting routine: thinplate=TRUE (the default) fits a thinplate spline, thinplate=FALSE fits independent smooth splines. If you have too few data points you may have to specify thinplate=FALSE
controls the link function passed to ‘gam’: one of ‘gaussian’, ‘binomial’, or ‘poisson’
controls the smoothness of the fit from gam
the number of X and Y values to use in establishing a grid for use in surf
the size of cell to use in calculating the tensioned hull
the number of contours to draw in representing the tensioned hull
the line type to use in drawing tensioned hull contours
identifier labels for samples. Defaults to 1:n
color index for points or contours
size of contour interval labels
plot character: glyph to plot
character expansion factor: size of plotted characters
the number of iterations to use in estimating the probability of the observed density
specific levels for contours in thull
arguments to pass to the plot function
Function ‘plotid’ returns a vector of row numbers of identified plots
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’, and ‘surf’ 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.
Function ‘density’ calculates the fraction of points within the convex hull that belong to the specified type.
Function ‘surf’ calculates and plots fitted surfaces for logical or
quantitative variables. The function employs the gam
function to fit a variable to the ordination coordinates, and to predict the
values at all grid points. The grid is established with the
‘expand.grid’ function, and the grid is then specified in a call to
‘predict.gam’. The predicted values are trimmed to the the convex hull
of the data, and the contours are fit by ‘contour’. 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 ‘thull’ calculates a tensioned hull for a specific variable on the NMDS. A tensioned hull is a minimum volume container. The grain size must be specified as a fraction of the units of the NMDS, with larger values generating smoother representations, and smaller numbers a more resolved container. ‘thull’ returns an invisible object of class ‘thull’ which has an associated plot function. Plotting the thull object produces a colored surface representation of the thull with optional contour lines.
# NOT RUN {
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))
# }
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