vegan: plot.cca – R documentation

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plot.cca

Plot or Extract Results of Constrained Correspondence Analysis or Redundancy Analysis

Description

Functions to plot or extract results of constrained correspondence analysis (cca), redundancy analysis (rda) or constrained analysis of principal coordinates (capscale).

Usage

## S3 method for class 'cca'
plot(x, choices = c(1, 2), display = c("sp", "wa", "cn"),
     scaling = "species", type, xlim, ylim, const,
     correlation = FALSE, hill = FALSE, ...)
## S3 method for class 'cca'
text(x, display = "sites", labels, choices = c(1, 2),
     scaling = "species", arrow.mul, head.arrow = 0.05, select, const,
     axis.bp = FALSE, correlation = FALSE, hill = FALSE, ...)
## S3 method for class 'cca'
points(x, display = "sites", choices = c(1, 2),
       scaling = "species", arrow.mul, head.arrow = 0.05, select, const,
       axis.bp = FALSE, correlation = FALSE, hill = FALSE, ...)
## S3 method for class 'cca'
scores(x, choices = c(1,2), display = c("sp","wa","cn"),
       scaling = "species", hill = FALSE, ...)
## S3 method for class 'rda'
scores(x, choices = c(1,2), display = c("sp","wa","cn"),
       scaling = "species", const, correlation = FALSE, ...)
## S3 method for class 'cca'
summary(object, scaling = "species", axes = 6,
        display = c("sp", "wa", "lc", "bp", "cn"),
        digits = max(3, getOption("digits") - 3),
        correlation = FALSE, hill = FALSE, ...)
## S3 method for class 'summary.cca'
print(x, digits = x$digits, head = NA, tail = head, ...)
## S3 method for class 'summary.cca'
head(x, n = 6, tail = 0, ...)
## S3 method for class 'summary.cca'
tail(x, n = 6, head = 0, ...)
## S3 method for class 'cca'
labels(object, display, ...)

Arguments

`x, object`	A `cca` result object.
`choices`	Axes shown.
`display`	Scores shown. These must include some of the alternatives `species` or `sp` for species scores, `sites` or `wa` for site scores, `lc` for linear constraints or LC scores, or `bp` for biplot arrows or `cn` for centroids of factor constraints instead of an arrow, and `reg` for regression coefficients (a.k.a. canonical coefficients).
`scaling`	Scaling for species and site scores. Either species (`2`) or site (`1`) scores are scaled by eigenvalues, and the other set of scores is left unscaled, or with `3` both are scaled symmetrically by square root of eigenvalues. Corresponding negative values can be used in `cca` to additionally multiply results with √(1/(1-λ)). This scaling is know as Hill scaling (although it has nothing to do with Hill's rescaling of `decorana`). With corresponding negative values in `rda`, species scores are divided by standard deviation of each species and multiplied with an equalizing constant. Unscaled raw scores stored in the result can be accessed with `scaling = 0`. The type of scores can also be specified as one of `"none"`, `"sites"`, `"species"`, or `"symmetric"`, which correspond to the values `0`, `1`, `2`, and `3` respectively. Arguments `correlation` and `hill` in `scores.rda` and `scores.cca` respectively can be used in combination with these character descriptions to get the corresponding negative value.
`correlation, hill`	logical; if `scaling` is a character description of the scaling type, `correlation` or `hill` are used to select the corresponding negative scaling type; either correlation-like scores or Hill's scaling for PCA/RDA and CA/CCA respectively. See argument `scaling` for details.
`type`	Type of plot: partial match to `text` for text labels, `points` for points, and `none` for setting frames only. If omitted, `text` is selected for smaller data sets, and `points` for larger.
`xlim, ylim`	the x and y limits (min,max) of the plot.
`labels`	Optional text to be used instead of row names. If you use this, it is good to check the default labels and their order using `labels` command.
`arrow.mul`	Factor to expand arrows in the graph. Arrows will be scaled automatically to fit the graph if this is missing.
`head.arrow`	Default length of arrow heads.
`select`	Items to be displayed. This can either be a logical vector which is `TRUE` for displayed items or a vector of indices of displayed items.
`const`	General scaling constant to `rda` scores. The default is to use a constant that gives biplot scores, that is, scores that approximate original data (see `vignette` on ‘Design Decisions’ with `browseVignettes("vegan")` for details and discussion). If `const` is a vector of two items, the first is used for species, and the second item for site scores.
`axis.bp`	Draw `axis` for biplot arrows.
`axes`	Number of axes in summaries.
`digits`	Number of digits in output.
`n, head, tail`	Number of rows printed from the head and tail of species and site scores. Default `NA` prints all.
`...`	Parameters passed to other functions.

Details

Same plot function will be used for cca and rda. This produces a quick, standard plot with current scaling.

The plot function sets colours (col), plotting characters (pch) and character sizes (cex) to certain standard values. For a fuller control of produced plot, it is best to call plot with type="none" first, and then add each plotting item separately using text.cca or points.cca functions. These use the default settings of standard text and points functions and accept all their parameters, allowing a full user control of produced plots.

Environmental variables receive a special treatment. With display="bp", arrows will be drawn. These are labelled with text and unlabelled with points. The arrows have basically unit scaling, but if sites were scaled (scaling "sites" or "symmetric"), the scores of requested axes are adjusted relative to the axis with highest eigenvalue. With scaling = "species" or scaling = "none", the arrows will be consistent with vectors fitted to linear combination scores (display = "lc" in function envfit), but with other scaling alternatives they will differ. The basic plot function uses a simple heuristics for adjusting the unit-length arrows to the current plot area, but the user can give the expansion factor in mul.arrow. With display="cn" the centroids of levels of factor variables are displayed (these are available only if there were factors and a formula interface was used in cca or rda). With this option continuous variables still are presented as arrows and ordered factors as arrows and centroids. With display = "reg" arrows will be drawn for regression coefficients (a.k.a. canonical coefficients) of constraints and conditions. Biplot arrows can be interpreted individually, but regression coefficients must be interpreted all together: the LC score for each site is the sum of regressions displayed by arrows. The partialled out conditions are zero and not shown in biplot arrows, but they are shown for regressions, and show the effect that must be partialled out to get the LC scores. The biplot arrows are more standard and more easily interpreted, and regression arrows should be used only if you know that you need them.

If you want to have a better control of plots, it is best to construct the plot text and points commands which accept graphical parameters. It is important to remember to use the same scaling, correlation and hill arguments in all calls. The plot.cca command returns invisibly an ordiplot result object, and this will have consistent scaling for all its elements. The easiest way for full control of graphics is to first set up the plot frame using plot with type = "n" and all needed scores in display and save this result. The points and text commands for ordiplot will allow full graphical control (see section Examples). Utility function labels returns the default labels in the order they are applied in text.

Function summary lists all scores and the output can be very long. You can suppress scores by setting axes = 0 or display = NA or display = NULL. You can display some first or last (or both) rows of scores by using head or tail or explicit print command for the summary.

Palmer (1993) suggested using linear constraints (“LC scores”) in ordination diagrams, because these gave better results in simulations and site scores (“WA scores”) are a step from constrained to unconstrained analysis. However, McCune (1997) showed that noisy environmental variables (and all environmental measurements are noisy) destroy “LC scores” whereas “WA scores” were little affected. Therefore the plot function uses site scores (“WA scores”) as the default. This is consistent with the usage in statistics and other functions in R (lda, cancor).

Value

The plot function returns invisibly a plotting structure which can be used by function identify.ordiplot to identify the points or other functions in the ordiplot family.

Author(s)

Jari Oksanen

Examples

data(dune)
data(dune.env)
mod <- cca(dune ~ A1 + Moisture + Management, dune.env)
## better control -- remember to set scaling etc identically
plot(mod, type="n", scaling="sites")
text(mod, dis="cn", scaling="sites")
points(mod, pch=21, col="red", bg="yellow", cex=1.2, scaling="sites")
text(mod, "species", col="blue", cex=0.8, scaling="sites")
## catch the invisible result and use ordiplot support - the example
## will make a biplot with arrows for species and correlation scaling
pca <- rda(dune)
pl <- plot(pca, type="n", scaling="sites", correlation=TRUE)
with(dune.env, points(pl, "site", pch=21, col=1, bg=Management))
text(pl, "sp", arrow=TRUE, length=0.05, col=4, cex=0.6, xpd=TRUE)
with(dune.env, legend("bottomleft", levels(Management), pch=21, pt.bg=1:4, bty="n"))
## Limited output of 'summary'
head(summary(mod), tail=2)
## Scaling can be numeric or more user-friendly names
## e.g. Hill's scaling for (C)CA
scrs <- scores(mod, scaling = "sites", hill = TRUE)
## or correlation-based scores in PCA/RDA
scrs <- scores(rda(dune ~ A1 + Moisture + Management, dune.env),
               scaling = "sites", correlation = TRUE)

vegan

Community Ecology Package

v2.5-7

GPL-2

Authors

Jari Oksanen, F. Guillaume Blanchet, Michael Friendly, Roeland Kindt, Pierre Legendre, Dan McGlinn, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens, Eduard Szoecs, Helene Wagner

Initial release