getTreeResults {treekoR} | R Documentation |
getTreeResults
getTreeResults(testedTree, sort_by = "parent")
testedTree |
a ggtree object outputed from testTree() |
sort_by |
whether to sort by p-values testing via proportions to parent or p-values testing via absolute proportions. Values can can be c(NA, "parent", "all") |
a dataframe with hierarchical tree nodes, corresponding clusters and corresponding significance testing results
library(SingleCellExperiment) data(COVIDSampleData) sce <- DeBiasi_COVID_CD8_samp exprs <- t(assay(sce, "exprs")) clusters <- colData(sce)$cluster_id classes <- colData(sce)$condition samples <- colData(sce)$sample_id clust_tree <- getClusterTree(exprs, clusters, hierarchy_method="hopach") tested_tree <- testTree(clust_tree$clust_tree, clusters=clusters, samples=samples, classes=classes, pos_class_name=NULL) res_df <- getTreeResults(tested_tree) head(res_df, 10)