mm_Phenotype {moRphomenses} | R Documentation |
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)
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. |
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 dendextend::cutree for a given height.ctk_grps - If
ctk_grps
is specified, a vector defining group membership (as integer); the results of clustering using dendextend::cutree for a given number of clusters.