hopachToPhylo: hopachToPhylo

In adam2o1o/treekoR: Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

hopachToPhylo

Description

hopachToPhylo

Usage

hopachToPhylo(res)

Arguments

res	an object returned from the runHOPACH() function

Value

a phylogram converted from the outputted list from the runHOPACH function

Examples

library(SingleCellExperiment)
library(data.table)
data(COVIDSampleData)

sce <- DeBiasi_COVID_CD8_samp
exprs <- t(assay(sce, "exprs"))
clusters <- colData(sce)$cluster_id
classes <- colData(sce)$condition
samples <- colData(sce)$sample_id

clust_med_dt <- as.data.table(exprs)
clust_med_dt[, cluster_id := clusters]
res <- clust_med_dt[, lapply(.SD, median, na.rm=TRUE), by=cluster_id]
res2 <- res[,.SD, .SDcols = !c('cluster_id')]

hopach_res <- runHOPACH(as.data.frame(scale(res2)))
phylo <- hopachToPhylo(hopach_res)

adam2o1o/treekoR documentation built on June 2, 2023, 11:42 p.m.