## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup-------------------------------------------------------------------- # Load required packages suppressPackageStartupMessages({ library(treekoR) library(SingleCellExperiment) library(ggtree) }) ## ----eval=F------------------------------------------------------------------- # # Install the development version from GitHub: # # install.packages("devtools") # devtools::install_github("adam2o1o/treekoR") # library(treekoR) ## ----------------------------------------------------------------------------- data(COVIDSampleData) sce <- DeBiasi_COVID_CD8_samp ## ----------------------------------------------------------------------------- exprs <- t(assay(sce, "exprs")) clusters <- colData(sce)$cluster_id classes <- colData(sce)$condition samples <- colData(sce)$sample_id ## ----------------------------------------------------------------------------- clust_tree <- getClusterTree(exprs, clusters, hierarchy_method="hopach") ## ----------------------------------------------------------------------------- tested_tree <- testTree(phylo=clust_tree$clust_tree, clusters=clusters, samples=samples, classes=classes, pos_class_name=NULL) ## ----------------------------------------------------------------------------- res_df <- getTreeResults(tested_tree) head(res_df, 10) ## ----------------------------------------------------------------------------- plotInteractiveHeatmap(tested_tree, clust_med_df = clust_tree$median_freq, clusters=clusters) ## ----------------------------------------------------------------------------- clust_tree <- getClusterTree(exprs, clusters, hierarchy_method="average") tested_tree <- testTree(clust_tree$clust_tree, clusters=clusters, samples=samples, classes=classes, pos_class_name=NULL) plotInteractiveHeatmap(tested_tree, clust_med_df = clust_tree$median_freq, clusters=clusters) ## ----------------------------------------------------------------------------- clust_tree <- getClusterTree(exprs, clusters, hierarchy_method="hopach") tested_tree_edgeR <- testTree(clust_tree$clust_tree, clusters=clusters, samples=samples, classes=classes, sig_test="edgeR", pos_class_name="COV") plotInteractiveHeatmap(tested_tree_edgeR, clust_med_df = clust_tree$median_freq, clusters=clusters) ## ----------------------------------------------------------------------------- head(tested_tree_edgeR$data[,c("parent", "node", "isTip", "clusters", "FDR_parent", "FDR_total")]) ## ----------------------------------------------------------------------------- prop_df <- getCellProp(phylo=clust_tree$clust_tree, clusters=clusters, samples=samples, classes=classes) head(prop_df[,1:8]) ## ----------------------------------------------------------------------------- means_df <- getCellGMeans(clust_tree$clust_tree, exprs=exprs, clusters=clusters, samples=samples, classes=classes) head(means_df[,1:8]) ## ----------------------------------------------------------------------------- sessionInfo()