plotInteractiveHeatmap: Title

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

Title

Description

This function takes a hierarchical tree which has been tested for proportion to all and proportion to parent cluster

Usage

plotInteractiveHeatmap(
  testedTree,
  clust_med_df,
  clusters,
  svg_width = 13,
  svg_height = 9,
  tr_offset = 0.3,
  tr_font_size = 2,
  tr_point_size = 1.5,
  tr_col_high = "#00c434",
  tr_col_low = "purple",
  tr_col_mid = "ivory2",
  hm_offset = 1,
  hm_tile_width = 1,
  hm_expand_y_lim = 20,
  hm_col_high = "#cc2010",
  hm_col_mid = "#fff8de",
  hm_col_low = "#66a6cc",
  fb_offset = 0.75,
  fb_bar_length = 3,
  fb_bar_width = 0.4,
  fb_freq_labels = FALSE
)

Arguments

testedTree	a ggtree object that has been run through the testTree
clust_med_df	a dataframe with the cluster medians. The rownumbers of the clusters median data frame should correspond to the nodes in the phylo tree. The column names should also correspond to the labels you want to use
clusters	a vector representing the cell type or cluster of each cell (can be character or numeric)
svg_width	width of svg canvas
svg_height	height of svf canvas
tr_offset	distance between leaf nodes on the tree and their labels
tr_font_size	font size of leaf labels
tr_point_size	size of each node in the tree
tr_col_high	colour used for high test statistics, coloured on the nodes and branches of the tree
tr_col_low	colour used for low test statistics, coloured on the nodes and branches of the tree
tr_col_mid	colour used for medium test statistics, coloured on the nodes and branches of the tree
hm_offset	distance between the tree and the heatmap
hm_tile_width	width of each tile in the heatmap
hm_expand_y_lim	white space below heatmap
hm_col_high	colour used for large values on heatmap
hm_col_mid	colour used for medium values on heatmap
hm_col_low	colour used for low values on heatmap
fb_offset	distance between the heatmap and frequency bars
fb_bar_length	length of bar with max frequency
fb_bar_width	width of each frequency bar
fb_freq_labels	boolean indicated whether or not to show frequency bar labels

Value

an interactive ggplot object containing the hierarchical tree of clusters coloured by significance testing results, with corresponding heatmap and a scatterplot comparing significance whne testing using proportions to parent vs. absolute proportions

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)

plotInteractiveHeatmap(tested_tree,
                       clust_med_df = clust_tree$median_freq,
                       clusters=clusters)

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