# Load required packages
suppressPackageStartupMessages({
library(treekoR)
library(SingleCellExperiment)
library(ggtree)
})# Install the development version from GitHub:
# install.packages("devtools")
devtools::install_github("adam2o1o/treekoR")
library(treekoR)treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data, to find robust and interpretable associations between cell subsets and patient clinical end points. This is achieved by deriving the tree structure of cell clusters, followed by measuring the %parent (proportions of each node in the tree relative to the number of cells belonging to the immediate parent node), in addition to the %total (proportion of cells in each node relative to all cells). These proportions are then used in significance testing and classification models to determine which cell subpopulation proportions most correlated with the patient clinical outcome of interest. treekoR then provides an interactive visualisation which helps to highlight these results.
SingleCellExperiment containing samples of flow cytometry expression data from 39 patients. This data represents a subset of a dataset that was originally used by De Biasi et al. (2020) for the characterisation of CD8+ T cells, comparing between COVID-19 patients and healthy controls.data(COVIDSampleData)
sce <- DeBiasi_COVID_CD8_samptreekoR requires the following information in the variables:
exprs: Single cell expression data (\(n \times p\)), where \(p\) is the number of markers, and \(n\) is the number of cellsclusters: a vector of length \(n\) representing the cell type or cluster of each cell (can be character or numeric)classes: a vector of length \(n\) containing the patient outcome/class each cell belongs tosamples: a vector of length \(n\) identifying the patient each cell belongs toIn this example: the clusters contain 100 clusters generated by FlowSOM; classes identify whether the cell belongs to a COVID-19 or healthy patient; and samples identify which cell the patient comes from.
exprs <- t(assay(sce, "exprs"))
clusters <- colData(sce)$cluster_id
classes <- colData(sce)$condition
samples <- colData(sce)$sample_idThe scaled median marker expression for each cluster is calculated which is used to construct a hierarchical tree.
In this step, the choice of hierarchical aggregation method (which determines the structure of the tree) is determined. By default the framework chooses HOPACH to construct the tree via the hierarchy_method argument, however any of the methods in hclust can be used (see 3.5.1).
clust_tree <- getClusterTree(exprs,
clusters,
hierarchy_method="hopach")Proportions of each cell cluster in the tree are calculated - both the proportion relative to all and proportion relative to the hierarchical parent. These proportions are used in a two sample t-test, testing for equal means between the patient clinical outcome using both types of proportions.
tested_tree <- testTree(phylo=clust_tree$clust_tree,
clusters=clusters,
samples=samples,
classes=classes,
pos_class_name=NULL)node: unique identifier for each node in the hierarchical treeparent: the node of the parentisTip: whether the node is a leaf node in the treeclusters: the clusters belonging to the corresponding nodestat_all: test statistic obtained from testing between conditions using the proportion of the node relative to all cells (%total) in each sample. pval_total is the corresponding p-value (unadjusted)stat_parent: test statistic obtained from testing between conditions using the proportion of the node relative to cells in the parent node (%parent) in each sample. pval_parent is the corresponding p-value (unadjusted)res_df <- getTreeResults(tested_tree)
head(res_df, 10)
#> parent node isTip clusters stat_total stat_parent pval_total
#> 51 139 51 TRUE 77 1.0823881 4.439944 0.290116635
#> 52 139 52 TRUE 66 -1.9247385 -4.439944 0.069760334
#> 63 147 63 TRUE 41 1.8107720 3.337019 0.080505219
#> 67 150 67 TRUE 32 1.7508315 3.229075 0.092603817
#> 136 135 136 FALSE 58, 67, 57 1.4290582 -3.198607 0.163963670
#> 71 150 71 TRUE 54 -2.3514750 -2.829766 0.033743471
#> 125 100 125 FALSE 85, 84, .... 2.7073249 2.707325 0.011833319
#> 20 115 20 TRUE 89 -0.7764417 -2.897438 0.446585533
#> 116 115 116 FALSE 59, 88, .... 3.0537776 2.897438 0.005462897
#> 140 100 140 FALSE 35, 43, .... -2.5102007 -2.510201 0.017809639
#> pval_parent
#> 51 0.0003193122
#> 52 0.0003193122
#> 63 0.0022734266
#> 67 0.0033277959
#> 136 0.0041906737
#> 71 0.0082310590
#> 125 0.0118333189
#> 20 0.0124821272
#> 116 0.0124821272
#> 140 0.0178096392The results of the previous steps are visualised by a coloured tree with a corresponding heatmap. The heatmap displays the median scaled marker expressions of each cluster to help understand what cell type each cluster may represent, and the tree not only reveals how clusters have been hierarchically aggregated, but is coloured on each node by the test statistic obtained when testing using the proportions relative to all of that node, with the branch connecting the child to the parent coloured by the test statistic obtained when testing using the proportions relative to parent of the child node.
plotInteractiveHeatmap(tested_tree,
clust_med_df = clust_tree$median_freq,
clusters=clusters)
#> Warning: Removed 1 rows containing missing values (`geom_interactive_point()`).