plotInteractiveHeatmap: Title

View source: R/visualiseTree.R

plotInteractiveHeatmapR Documentation

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.