changebio/MAGPA: Multivariate Analysis of Genotype–Phenotype Association and Visualization for 3D Image

The MAGPA (multivariate analysis of genotype–phenotype association) is a package of multivariate correlation analysis and an interactive visualization tool for 3D image. This package was implemented for genetic association analysis of facial phenotypes and visualization related results. In addition, it can also be used in genome-wide association analysis of other multivariate phenotypes, especially three-dimensional image data. It can not only receive the prepared features, but also preprocess the features with principal component analysis and automatically select the number of variables. The genotype should be a SnpMatrix, which is a special object holding large arrays of single nucleotide polymorphism (SNP). Then，canonical correlation analysis (CCA) is used to extract the linear combination of variables to maximize the correlation with each SNP. For the interactive visualization, visual3d is required to provide at least a reference of 3D image object and a vector, such as the phenotypic changes under different genotypes, which is highly customized. it can draw a 3D object with different style and gradient colors.

install.packages("remotes")
remotes::install_github("changebio/MAGPA")