printClusterAssignments: Writes samples to file based on community detection group...
In phemd: Phenotypic EMD for comparison of single-cell samples

Description Usage Arguments Details Value Examples

Takes vector of cluster assignments and phemdObj containing sample names and writes sample groups to file

1	printClusterAssignments(cluster_assignments, obj, dest, overwrite = FALSE)

`cluster_assignments`	Vector containing group assignments for each sample
`obj`	phemdObj object containing sample names in @snames slot
`dest`	Path to existing directory where output should be saved
`overwrite`	Boolean representing whether or not to overwrite contents of "dest" with output of printClusterAssignments

Order of samples in obj@snames is assumed to be the same as the order of group assignments in cluster_assignments

None

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)
printClusterAssignments(cluster_assignments, my_phemdObj_final, '.', overwrite=TRUE)