Plotting Routines For LabDSV Ordinations
A set of routines for plotting, highlighting points, or adding fitted surfaces to ordinations.
## S3 method for class 'dsvord'
plot(x, ax = 1, ay = 2, col = 1, title = "", pch = 1, ...)
## S3 method for class 'dsvord'
points(x, which, ax = 1, ay = 2, col = 2, pch = 1, cex = 1,
breaks=FALSE, ...)
## S3 method for class 'dsvord'
plotid(ord, ids = seq(1:nrow(ord$points)), ax = 1, ay = 2,
col = 1, ...)
## S3 method for class 'dsvord'
hilight(ord, overlay, ax = 1, ay = 2, title="",
cols=c(2,3,4,5,6,7), glyph=c(1,3,5), ...)
## S3 method for class 'dsvord'
chullord(ord, overlay, ax = 1, ay = 2, cols=c(2,3,4,5,6,7),
ltys = c(1,2,3), ...)
## S3 method for class 'dsvord'
ellip(ord, overlay, ax = 1, ay = 2, cols=c(2,3,4,5,6,7),
ltys = c(1,2,3), ...)
## S3 method for class 'dsvord'
surf(ord, var, ax = 1, ay = 2, thinplate = TRUE, col = 2,
labcex = 0.8, family = gaussian, gamma=1, grid=50, ...)
## S3 method for class 'dsvord'
thull(ord,var,grain,ax=1,ay=2,col=2,grid=51,nlevels=5,
levels=NULL,lty=1,
numitr=100,...)
## S3 method for class 'dsvord'
density(ord, overlay, ax = 1, ay = 2, cols = c(2, 3, 4, 5,
6, 7), ltys = c(1, 2, 3), numitr, ...)x |
an object of class ‘dsvord’ |
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 |
breaks |
a logical switch to control using variable glyph sizes in ‘points’ |
ord |
an object of class ‘dsvord’ |
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 |
ltys |
the sequence of line types to be used |
var |
a variable to be surfaced or tension hulled |
thinplate |
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 |
family |
controls the link function passed to ‘gam’: one of ‘gaussian’, ‘binomial’, ‘poisson’ or ‘nb’ |
gamma |
controls the smoothness of the fit from |
grid |
the number of X and Y values to use in establishing a grid for use in surf |
grain |
the size of cell to use in calculating the tensioned hull |
nlevels |
the number of contours to draw in representing the tensioned hull |
lty |
the line type to use in drawing tensioned hull contours |
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 |
numitr |
the number of iterations to use in estimating the probability of the observed density |
levels |
specific levels for contours in thull |
... |
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’, 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 ordination, 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 ‘ellip’ is passed a factor vector or integer vector, and plots minimal volume ellipses containingg all points within a class. By specifying values for arguments ‘cols’ and ‘ltys’ it is possible to control the sequence of colors and linetypes of the ellipses.
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 or ‘family='nb'’ to get a negative binomial fit.
Function ‘thull’ calculates a tensioned hull for a specific variable on the ordination. 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.
Function ‘plotid’ returns a vector of row numbers of identified plots
The contouring routine using
predict.gam follows ordisurf as
suggested by Jari Oksanen.
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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