colourTree {treekoR} | R Documentation

## colourTree

### Description

Adding statistical test results onto the tree by using colourful nodes and branches Takes a ggtree object with test results for each node and returns a ggtree graph object

### Usage

    colourTree(
      tree,
      point_size = 1.5,
      high = "#00c434",
      low = "purple",
      mid = "ivory2"
    )

### Arguments

`tree` | a tree plot created from the ggtree() function with p$data containing test statisic and p-
`point_size` | size of nodes in the tree
`high` | colour for large values
`low` | colour for low values
`mid` | colour for middle values

### Value

an interactive ggplot graph object, plotting the hierarchical tree of clusters with nodes and branches coloured by the significance testing results.

### Examples

    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)

    colourTree(tested_tree)

[Package treekoR version 1.2.1 Index]