getData: Extract data from a TreeHeatmap

In fionarhuang/treeclimbR: An algorithm to find optimal signal levels in a tree

Extract data from a TreeHeatmap

Description

Extract different elements of the data shown in a figure generated with TreeHeatmap, such as the heatmap itself, or the row and column names.

Usage

getData(
  tree_hm,
  type = c("heatmap", "row_name", "column_name", "title", "column_anno", "column_order",
    "column_split")
)

Arguments

tree_hm	The output of TreeHeatmap.
type	A character scalar indicating the type of information to extract. Should be one of "heatmap", "row_name", "column_name", "title", "column_anno", "column_order".

Value

A data.frame (if type is not "column_order"), or a vector of column names (if type is "column_order").

Author(s)

Ruizhu Huang

Examples

suppressPackageStartupMessages({
    library(TreeSummarizedExperiment)
    library(ggtree)
    library(ggplot2)
    library(scales)
    library(dplyr)
    library(ggnewscale)
})

## Load example data (tiny tree with corresponding count matrix)
tse <- readRDS(system.file("extdata", "tinytree_counts.rds",
                           package = "treeclimbR"))

## Aggregate counts for each of the highlighted subtrees
tseagg <- aggTSE(
    tse,
    rowLevel = c(13, 18,
                 setdiff(showNode(tinyTree, only.leaf = TRUE),
                         unlist(findDescendant(tinyTree, node = c(13, 18),
                                               only.leaf = TRUE)))))
ct <- SummarizedExperiment::assay(tseagg, "counts")
col_split <- ifelse(colnames(ct) %in% paste0("S", seq_len(5)), "A", "B")
names(col_split) <- colnames(ct)

## Prepare the tree figure
tree_fig <- ggtree(tinyTree, branch.length = "none",
                   layout = "rectangular") +
    geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
    geom_hilight(node = 13, fill = "blue", alpha = 0.3)
fig <- TreeHeatmap(
    tree = tinyTree, tree_fig = tree_fig, hm_data = ct,
    cluster_column = TRUE, column_split = col_split,
    column_anno = col_split, column_anno_gap = 0.6,
    column_anno_color = c(A = "red", B = "blue"),
    show_colnames = TRUE, colnames_position = "bottom",
    colnames_angle = 90, colnames_size = 2, colnames_offset_y = -0.2,
    show_title = TRUE, title_offset_y = 1.5, title_color = "blue"
)
fig

## Extract data for heatmap
df_hm <- getData(tree_hm = fig, type = "heatmap")

## Generate data to add a column annotation
ct <- df_hm |>
    dplyr::select(x, width, variable) |>
    dplyr::distinct()
set.seed(1)
ann <- matrix(sample(LETTERS[seq_len(2)], size = 3 * ncol(df_hm),
                     replace = TRUE),
              nrow = 3)
rownames(ann) <- paste0("g", seq_len(3))
colnames(ann) <- ct$variable
ann <- data.frame(ann) |>
       mutate(y = min(df_hm$y) - seq_len(nrow(ann)),
       label = rownames(ann))
df_ann <- tidyr::pivot_longer(
    ann, names_to = "variable",
    values_to = "value", cols = -c("y", "label")) |>
    left_join(ct)

## Add new column annotation
fig +
    new_scale_fill() +
    geom_tile(data = df_ann, aes(x, y-0.5,
                                 width = width, fill = value)) +
    scale_fill_viridis_d() +
    geom_text(data = df_ann, aes(x = min(x) - 1, y = y - 0.5,
                label = label))

fionarhuang/treeclimbR documentation built on Nov. 7, 2024, 4:17 a.m.