Phemd: Phemd class
In phemd: Phenotypic EMD for comparison of single-cell samples

The main PhEMD class to store single-cell expression data.

data: List of matrices, each of which represents a single-cell sample (num_cells x num_genes)
markers: Column names (e.g. genes) for each element (i.e. data matrix) in "data"
snames: Sample ID for each element in "data"
data_aggregate: Numeric matrix representing expression data for cells from all experimental conditions (rows = markers, cols = cells)
data_subsample_idx: List of vectors each representing the indices of elements in "data" that were subsampled and combined to form "data_aggregate"
subsampled_bool: Boolean represent whether or not subsampling was performed in the data aggregation process
monocle_obj: Data object of type "CellDataSet" that is the core Monocle data structure
data_cluster_weights: Matrix representing cell subtype relative frequencies for each sample (num_samples x num_genes)
emd_dist_mat: Matrix representing pairwise distances between each pair of cell subtypes
seurat_obj: Object of class "Seurat" that is the core Seurat data structure
phate_obj: Object of class "phate" that is the core PHATE data structure
experiment_ids: Vector of length num_samples representing the experiment (batch) in which the sample was profiled