compareSamples: Computes EMD distance matrix representing pairwise...

In KrishnaswamyLab/phemd: Phenotypic EMD for comparison of single-cell samples

Computes EMD distance matrix representing pairwise dissimilarity between samples

Description

Takes as input a Phemd object with cell subtype relative frequencies for each sample in @data_cluster_weights slot and ground distance matrix (representing cell subtype pairwise dissimilarity) in @emd_dist_mat slot. Returns distance matrix representing pairwise dissimilarity between samples

Usage

compareSamples(obj)

Arguments

obj	'Phemd' object containing cell subtype relative frequencies for each sample in @data_cluster_weights slot and ground distance matrix (representing cell subtype dissimilarity) in @emd_dist_mat slot

Details

Requires 'transport' and 'pracma' packages

Value

Distance matrix of dimension num_samples x num_samples representing pairwise dissimilarity between samples

Examples

my_phemdObj <- createDataObj(all_expn_data, all_genes, as.character(snames_data))
my_phemdObj_lg <- removeTinySamples(my_phemdObj, 10)
my_phemdObj_lg <- aggregateSamples(my_phemdObj_lg, max_cells=1000)
my_phemdObj_monocle <- embedCells(my_phemdObj_lg, data_model = 'gaussianff', sigma=0.02, maxIter=2)
my_phemdObj_monocle <- orderCellsMonocle(my_phemdObj_monocle)
my_phemdObj_final <- clusterIndividualSamples(my_phemdObj_monocle)
my_phemdObj_final <- generateGDM(my_phemdObj_final)
my_EMD_mat <- compareSamples(my_phemdObj_final)

KrishnaswamyLab/phemd documentation built on April 24, 2023, 3:50 p.m.