Quarto/R Script for Ventricular Shape Analysis: GPA Sliding Semilandmarks, Procrustes ANOVA, and Phenotypic Trajectory Testing (E7.5 vs E10.5; Control vs cKO)

This Quarto (.qmd) script reproduces the 3D ventricular geometric morphometrics workflow used in the study. It imports (i) an outputData.csv table containing per-sample landmark coordinates in columns named LM._X, LM._Y, LM._Z (with sample IDs in Sample_name), and (ii) a Sample_summary file mapping each Sample to experimental factors (Induction time and Group/Genotype). The script performs generalized Procrustes analysis (GPA) with sliding semilandmarks along a closed contour, runs a two-factor Procrustes ANOVA (Induction * Group) with permutation testing, performs phenotypic trajectory analysis comparing Control→cKO effects across induction stages (magnitude and trajectory angle), and generates a PCA morphospace plot with group convex hulls and centroid arrows (E7.5→E10.5).