generateGDM {phemd}R Documentation

Computes ground distance matrix based on cell embedding

Description

Takes as input a Phemd object with Monocle2 object (already embedded and ordered) in @monocle_obj slot. Returns updated object with ground distance matrix representing pairwise distance between 2 cell subtypes based on cell state embedding.

Usage

generateGDM(obj, cell_model = c("monocle2", "seurat"),
  expn_type = "aligned")

Arguments

obj

'Phemd' object containing Monocle2 object (already embedded and ordered) in @monocle_obj slot

cell_model

Method by which cell state was modeled (either "monocle2" or "seurat")

expn_type

Data type to use to determine cell-type dissimilarities

Details

embedCells and orderCellsMonocle need to be called before calling this function. Requires 'igraph' package

Value

Phemd object with ground distance matrix (to be used in EMD computation) in @data_cluster_weights slot

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)


[Package phemd version 1.0.0 Index]