ordiArrowTextXY: Support Functions for Drawing Vectors

Description Usage Arguments Details Value Author(s) Examples

Description

Support functions to assist with drawing of vectors (arrows) on ordination plots. ordiArrowMul finds the multiplier for the coordinates of the head of the vector such that they occupy fill proportion of the plot region. ordiArrowTextXY finds coordinates for the locations of labels to be drawn just beyond the head of the vector.

Usage

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ordiArrowTextXY(x, labels, display, choices = c(1,2),
                rescale = TRUE, fill = 0.75, at = c(0,0), ...)
ordiArrowMul(x, at = c(0,0), fill = 0.75,
             display, choices = c(1,2), ...)

Arguments

x

An R object, from which scores can determine suitable ordination scores or an object created by envfit, or a two-column matrix of coordinates of arrow heads on the two plot axes.

labels

Change plotting labels. A character vector of labels for which label coordinates are sought. If not supplied, these will be determined from the row names of x, or scores(x, ...) if required. If either of these are not defined, suitable labels will be generated.

display

a character string known to scores or one of its methods which indicates the type of scores to extract. In fitting functions these are ordinary site scores or linear combination scores ("lc") in constrained ordination (cca, rda, capscale). If x was created by envfit then display can not be set by the user and takes the value "vectors". Ignored if x is a matrix.

choices

Axes to be plotted.

rescale

logical; should the coordinates in or extracted from x be rescaled to fill fill proportion of the plot region? The default is to always rescale the coordinates as this is usually desired for objects x from which coordinates are retrieved. If supplying x a 2-column matrix that has already been rescaled, then set this to FALSE.

fill

numeric; the proportion of the plot to fill by the span of the arrows.

at

The origin of fitted arrows in the plot. If you plot arrows in other places than origin, you probably have to specify arrrow.mul.

...

Parameters passed to scores, and strwidth and strheight.

Details

ordiArrowMul finds a multiplier to scale a bunch of arrows to fill an ordination plot, and ordiArrowTextXY finds the coordinates for labels of these arrows. NB., ordiArrowTextXY does not draw labels; it simply returns coordinates at which the labels should be drawn for use with another function, such as text.

Value

For ordiArrowTextXY, a 2-column matrix of coordinates for the label centres in the coordinate system of the currently active plotting device.

For ordiArrowMul, a length-1 vector containing the scaling factor.

Author(s)

Jari Oksanen, with modifications by Gavin L. Simpson

Examples

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    ## Scale arrows by hand to fill 80% of the plot
    ## Biplot arrows by hand
    data(varespec, varechem)
    ord <- cca(varespec ~ Al + P + K, varechem)
    plot(ord, display = c("species","sites"))

    ## biplot scores
    bip <- scores(ord, choices = 1:2, display = "bp")

    ## scaling factor for arrows to fill 80% of plot
    (mul <- ordiArrowMul(bip, fill = 0.8))
    bip.scl <- bip * mul                    # Scale the biplot scores
    labs <- rownames(bip)                   # Arrow labels

    ## calculate coordinate of labels for arrows
    (bip.lab <- ordiArrowTextXY(bip.scl, rescale = FALSE, labels = labs))

    ## draw arrows and text labels
    arrows(0, 0, bip.scl[,1], bip.scl[,2], length = 0.1)
    text(bip.lab, labels = labs)

    ## Handling of ordination objects directly
    mul2 <- ordiArrowMul(ord, display = "bp", fill = 0.8)
    stopifnot(all.equal(mul, mul2))

Example output

Loading required package: permute
Loading required package: lattice
This is vegan 2.5-7
[1] 2.092173
         [,1]       [,2]
Al  1.9062057 -0.3555568
P  -0.9298005 -1.6652122
K  -1.0078568 -0.3768152

vegan documentation built on Jan. 8, 2021, 2:12 a.m.