plot_NMDS: NMDS plot unsing grindr layers

In Momocs: Morphometrics using R

NMDS plot unsing grindr layers

Description

Quickly vizualise MDS and NMDS objects and build customs plots using the layers. See examples.

Usage

plot_NMDS(
  x,
  f = NULL,
  axes = c(1, 2),
  points = TRUE,
  points_transp = 1/4,
  chull = TRUE,
  chullfilled = FALSE,
  labelgroups = FALSE,
  legend = TRUE,
  title = "",
  box = TRUE,
  axesnames = TRUE,
  palette = pal_qual
)

plot_MDS(
  x,
  f = NULL,
  axes = c(1, 2),
  points = TRUE,
  points_transp = 1/4,
  chull = TRUE,
  chullfilled = FALSE,
  labelgroups = FALSE,
  legend = TRUE,
  title = "",
  box = TRUE,
  axesnames = TRUE,
  palette = pal_qual
)

Arguments

x	the result of MDS or NMDS
f	factor specification to feed fac_dispatcher
axes	numeric of length two to select PCs to use (c(1, 2) by default)
points	logical whether to draw this with layer_points
points_transp	numeric to feed layer_points (default:0.25)
chull	logical whether to draw this with layer_chull
chullfilled	logical whether to draw this with layer_chullfilled
labelgroups	logical whether to draw this with layer_labelgroups
legend	logical whether to draw this with layer_legend
title	character if specified, fee layer_title (default to "")
box	logical whether to draw this using layer_box
axesnames	logical whether to draw this using layer_axesnames
palette	color palette to use col_summer by default

Value

a plot

See Also

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

Examples

### First prepare an NMDS object
x <- bot %>% efourier %>% NMDS

plot_NMDS(x)
plot_NMDS(x, ~type) %>% layer_stars() %>% layer_labelpoints()

### Same on MDS object
x <- bot %>% efourier %>% MDS

plot_MDS(x)
plot_MDS(x, ~type) %>% layer_stars() %>% layer_labelpoints()

Momocs documentation built on Nov. 13, 2023, 5:07 p.m.