getSampleHistsByCluster {phemd} | R Documentation |
Gets relative frequency ("weights") of cell subtypes ("bins" or "signatures") in each single-cell sample
getSampleHistsByCluster( myobj, cluster_assignments, cell_model = c("monocle2", "seurat") )
myobj |
phemdObj object containing cell subtype relative frequency in @data_cluster_weights slot |
cluster_assignments |
Vector containing group assignments for each sample in myobj |
cell_model |
Method by which cell state was modeled (either "monocle2" or "seurat") |
groupSamples
must be called before calling this function. Saves plots in directory called "individual_inhibs"
List of lists, with outer list representing sample cluster ID and inner list representing cell subtype frequencies of given sample
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) cluster_assignments <- groupSamples(my_EMD_mat, distfun = 'hclust', ncluster=4) weights_by_cluster <- getSampleHistsByCluster(my_phemdObj_final, cluster_assignments)