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Momocs (version 1.2.9)

layers: grindr layers for multivariate plots

Description

Useful layers for building custom mutivariate plots using the cheapbabi approach. See examples.

Usage

layer_frame(x, center_origin = TRUE, zoom = 0.9)

layer_axes(x, col = "#999999", lwd = 1/2, ...)

layer_grid(x, col = "#999999", lty = 3, grid = 3, ...)

layer_box(x, border = "#e5e5e5", ...)

layer_fullframe(x, ...)

layer_points(x, pch = 20, cex = 4/log1p(nrow(x$xy)), transp = 0, ...)

layer_morphospace(x, position = c("range", "full", "circle", "xy", "range_axes", "full_axes")[1], nb = 12, nr = 6, nc = 5, rotate = 0, size = 0.9, col = "#999999", flipx = FALSE, flipy = FALSE, draw = TRUE, ...)

layer_ellipses(x, conf = 0.5, lwd = 1, alpha = 0, ...)

layer_ellipsesfilled(x, conf = 0.5, lwd = 1, alpha = 0, ...)

layer_ellipsesaxes(x, conf = 0.5, lwd = 1, alpha = 0, ...)

layer_chull(x, ...)

layer_chullfilled(x, alpha = 0.8, ...)

layer_stars(x, alpha = 0.5, ...)

layer_delaunay(x, ...)

layer_density(x, levels_density = 20, levels_contour = 4, alpha = 1/3, n = 200, density = TRUE, contour = TRUE)

layer_labelpoints(x, col = par("fg"), cex = 2/3, font = 1, abbreviate = FALSE, ...)

layer_labelgroups(x, col = par("fg"), cex = 3/4, font = 2, rect = TRUE, alpha = 1/4, abbreviate = FALSE, ...)

layer_rug(x, size = 1/200, ...)

layer_title(x, title = "", cex = 3/4, ...)

layer_axesnames(x, cex = 3/4, name = "Axis", ...)

layer_eigen(x, nb_max = 5, cex = 1/2, ...)

layer_axesvar(x, cex = 3/4, ...)

layer_legend(x, probs = seq(0, 1, 0.25), cex = 3/4, ...)

Arguments

x

a list, typically returned by plot_PCA

center_origin

logical whether to center the origin (default TRUE)

zoom

numeric to change the zoom (default 0.9)

col

color (hexadecimal) to use for drawing components

lwd

linewidth for drawing components

...

additional options to feed core functions for each layer

lty

linetype for drawing components

grid

numeric number of grid to draw

border

color (hexadecimal) to use to draw border

pch

to use for drawing components

cex

to use for drawing components

transp

transparency to use (min: 0 defaut:0 max:1)

position

one of range, full, circle, xy, range_axes, full_axes) to feed morphospace_positions (default range)

nb

numeric total number of shapes when position="circle" (default 12)

nr

numeric number of rows to position shapes (default 6)

nc

numeric number of columns to position shapes (default 5)

rotate

numeric angle (in radians) to rotate shapes when displayed on the morphospace (default 0)

size

numeric size to use to feed coo_template (default 0.9)

flipx

logical whether to flip shapes against the x-axis (default FALSE)

flipy

logical whether to flip shapes against the y-axis (default FALSE)

draw

logical whether to draw shapes (default TRUE)

conf

numeric between 0 and 1 for confidence ellipses

alpha

numeric between 0 and 1 for the transparency of components

levels_density

numeric number of levels to use to feed MASS::kde2d

levels_contour

numeric number of levels to use to feed graphics::contour

n

numeric number of grid points to feed MASS::kde2d

density

logical whether to draw density estimate

contour

logical whether to draw contour lines

font

to feed text

abbreviate

logical whether to abbreviate names

rect

logical whether to draw a rectangle below names

title

to add to the plot (default "")

name

to use on axes (default "Axis")

nb_max

numeric number of eigen values to display (default 5)

probs

numeric sequence to feed stats::quantile and to indicate where to draw ticks and legend labels

See Also

grindr_drawers

Other grindr: drawers, mosaic_engine, papers, pile, plot_PCA