getSampleHistsByCluster: Gets cell subtype frequency histograms for each sample by...

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

Gets cell subtype frequency histograms for each sample by cluster ID

Description

Gets relative frequency ("weights") of cell subtypes ("bins" or "signatures") in each single-cell sample

Usage

getSampleHistsByCluster(
  myobj,
  cluster_assignments,
  cell_model = c("monocle2", "seurat")
)

Arguments

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")

Details

groupSamples must be called before calling this function. Saves plots in directory called "individual_inhibs"

Value

List of lists, with outer list representing sample cluster ID and inner list representing cell subtype frequencies of given sample

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)
cluster_assignments <- groupSamples(my_EMD_mat, distfun = 'hclust', ncluster=4)
weights_by_cluster <- getSampleHistsByCluster(my_phemdObj_final, cluster_assignments)

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