layers: grindr layers for multivariate plots

In vbonhomme/Momocs: Morphometrics using R

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_ticks(x, col = "#333333", cex = 3/4, lwd = 3/4, ...)

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_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_histogram_2(x, freq = FALSE, breaks, split = FALSE, transp = 0)

layer_density_2(x, bw, split = FALSE, rug = TRUE, transp = 0)

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
cex	to use for drawing components
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
transp	transparency to use (min: 0 defaut:0 max:1)
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
size	numeric as a fraction of graphical window (default: 1/200)
freq	logicalto feed⁠[hist] (default:⁠FALSE')
breaks	to feed hist (default: calculated on the pooled values)
split	logical whether to split the two distributions into two plots
bw	to feed density (default: stats::bw.nrd0)
rug	logical whether to add rug (default: TRUE)
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

Value

a drawing layer

See Also

grindr_drawers

Other grindr: drawers, layers_morphospace, mosaic_engine(), papers, pile(), plot_LDA(), plot_NMDS(), plot_PCA()

vbonhomme/Momocs documentation built on Nov. 13, 2023, 8:54 p.m.