mm_Phenotype: Generate Phenotypes

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

Generate Phenotypes

Description

Partition sample into clusters, based on information from

Usage

mm_Phenotype(
  dat,
  kgrps,
  cuttree_h = NULL,
  cuttree_k = NULL,
  plot_figs = TRUE,
  reset_par = TRUE
)

Arguments

dat	Either an Array of shape data, an mmPCA object, or an mmDiag object.
kgrps	A non-negative integer of sub-groups to draw. kgrps=1 will provide results for the whole input dat.
cuttree_h	Optional. Draw clusters by splitting the tree at a given height, h.
cuttree_k	Optional. Draw clsuters by splitting the tree into number of branches, k
plot_figs	Optional. Default = TRUE, plot phenotypes for each set(s) of subgroups.
reset_par	Optional, default = TRUE. If false, do not reset graphic parameters in order to create complex plots.

Value

If plot_figs=TRUE (Default), plot associated graphs and return a list containing:

• ALN - an array containing aligned and scaled landmark data, the output of mm_ArrayData

• PCA - PC scores, eigenvalues, and shape visualizations, the output of mm_CalcShapespace

• TREE - Dendrogram of PC scores, the output of mm_Diagnostics

• k_grps - If kgrps is specified, a vector defining group membership (as integer); the results of k-means clustering based on PC scores.

• cth_grps - If cth_grps is specified, a vector defining group membership (as integer); the results of clustering using stats::cutree for a given height.

• ctk_grps - If ctk_grps is specified, a vector defining group membership (as integer); the results of clustering using stats::cutree for a given number of clusters.

ehrlichd/moRphomenses documentation built on Jan. 9, 2025, 6:29 p.m.