mm_VizShapespace: Visualize PC axes

In ehrlichd/moRphomenses: Geometric Morphometric Tools to Align, Scale, and Compare "Shape" of Menstrual Cycle Hormones

Visualize PC axes

Description

Plot a scatterplot and vizualize shape change across the X axis.

Usage

mm_VizShapespace(
  mmPCA,
  xPC = 1,
  yPC = 2,
  yr = c(0, 1.1),
  cols = NULL,
  title = "",
  png_dir = NULL
)

Arguments

mmPCA	Output of mm_CalcShapespace, containing a PCA object with PC shapes
xPC	The PC to be plotted on the x axis. If yPC is left null, a univariate density distribution will be plotted with min/max shapes.
yPC	The PC to be plotted on the y axis.
yr	The y-xis range, in the format c(0,1)
cols	A vector of colors of length n, for use in scatterplot.
title	To be used for the plot
png_dir	A file path to a directory in which to save out PNG figures. Names will be automatically assigned based on input PC(s).

Details

Meant to be a quick diagnostic plot with minimal customization.

Value

Produces a series of plots to visualize PCA analysis. If png_dir is specified, function will save out .png files. Otherwise plots will be displayed in the default plot window.

ehrlichd/moRphomenses documentation built on Dec. 13, 2024, 8:36 a.m.