TreeHeatmap: Generate a heatmap corresponding to an arbitrary aggregation...

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

Generate a heatmap corresponding to an arbitrary aggregation level of a tree

Description

Generate a heatmap corresponding to an arbitrary aggregation level of a tree.

Usage

TreeHeatmap(
  tree,
  tree_fig,
  hm_data,
  tree_hm_gap = 0,
  rel_width = 1,
  cell_line_color = NA,
  cell_line_size = 0,
  column_order = NULL,
  column_split = NULL,
  column_split_gap = 0.2,
  column_split_label = NULL,
  split_label_fontface = "bold",
  split_label_color = "black",
  split_label_size = 3,
  split_label_angle = 0,
  split_label_offset_x = 0,
  split_label_offset_y = 2,
  split_label_hjust = 0.5,
  split_label_vjust = 0,
  column_anno = NULL,
  column_anno_size = 1,
  column_anno_color = NULL,
  column_anno_gap = 0.1,
  legend_title_hm = "Expression",
  legend_title_column_anno = "group",
  show_colnames = FALSE,
  colnames_position = "top",
  colnames_angle = 0,
  colnames_offset_x = 0,
  colnames_offset_y = 0,
  colnames_size = 4,
  colnames_hjust = 0.5,
  show_rownames = FALSE,
  rownames_position = "right",
  rownames_angle = 0,
  rownames_offset_x = 0,
  rownames_offset_y = 0,
  rownames_size = 4,
  rownames_hjust = 0.5,
  rownames_label = NULL,
  show_title = FALSE,
  title_hm = "First heatmap",
  title_fontface = "bold",
  title_color = "black",
  title_size = 3,
  title_angle = 0,
  title_offset_x = 0,
  title_offset_y = 2,
  title_hjust = 0.5,
  cluster_column = FALSE,
  dist_method = "euclidean",
  hclust_method = "ave",
  show_row_tree = TRUE
)

Arguments

tree	A phylo object.
tree_fig	A ggtree object corresponding to tree. This will be used to represent the tree in the resulting figure.
hm_data	A data.frame with the values to show in the heatmap. The row names should correspond to the nodes of tree.
tree_hm_gap	A numeric scalar specifying the gap between the tree and the heatmap.
rel_width	A numeric scalar specifying the width of heatmap relative to the width of the tree. For example, if rel_width = 1, the width of the heatmap is the same as the width of the tree.
cell_line_color	A color for the lines separating cells in the heatmap.
cell_line_size	A numeric scalar specifying the line width for lines separating cells in the heatmap.
column_order	A character vector specifying the display order of the columns in the heatmap. Should correspond to the column names of hm_data. Ignored when column_split is provided.
column_split	A named character vector that provides the grouping information used to split the columns in the heatmap. The names should correspond to the column names of hm_data.
column_split_gap	A numeric scalar specifying the gap between the groups of split columns in the heatmap.
column_split_label	A named character vector to label the column split. The names should correspond to the values in column_split.
split_label_fontface	The fontface of the labels of the column split.
split_label_color	The color of the the labels of the column split.
split_label_size	The size of the the labels of the column split.
split_label_angle	The angle of the the labels of the column split.
split_label_offset_x	A numeric value to shift the labels of the column split along the x-axis.
split_label_offset_y	A numeric value to shift the labels of the column split along the y-axis.
split_label_hjust	The horizontal justification for the labels of the column split: e.g. 0 (left aligned); 0.5 (centered); 1 (right aligned).
split_label_vjust	Similar to split_label_hjust, but controls vertical justification.
column_anno	A named vector to specify labels that are used to annotate the columns of heatmap.
column_anno_size	A numeric value to specify the size of the annotation bar.
column_anno_color	A named vector to specify colors that are used to annotate the columns of the heatmap.
column_anno_gap	A numeric value to specify the gap between the column annotation bar and the heatmap.
legend_title_hm	The legend title of the heatmap.
legend_title_column_anno	The legend title of the column annotation.
show_colnames	A logical value to specify whether column names should be displayed.
colnames_position	The position of column names, either "top" or "bottom".
colnames_angle	A numeric scalar specifying the angle of column names.
colnames_offset_x	A numeric value to shift column names on the x-axis.
colnames_offset_y	A numeric value to shift column names on the y-axis.
colnames_size	A numeric value to specify the size of column names.
colnames_hjust	The horizontal justification for column names: e.g. 0 (left aligned); 0.5 (centered); 1 (right aligned).
show_rownames	A logical value to specify whether row names should be displayed.
rownames_position	The position of the row names, either "right" or "left".
rownames_angle	A numeric value specifying the angle of row names.
rownames_offset_x	A numeric value to shift row names on the x-axis.
rownames_offset_y	A numeric value to shift row names on the y-axis.
rownames_size	A numeric value to specify the size of row names.
rownames_hjust	The horizontal justification for row names: e.g. 0 (left aligned); 0.5 (centered); 1 (right aligned).
rownames_label	A named vector to annotate the rows of the heatmap instead of the row names of hm_data.
show_title	A logical value to specify whether the title should be displayed.
title_hm	The title of the heatmap.
title_fontface	The fontface of the title.
title_color	The color of the title.
title_size	The size of the title.
title_angle	The angle of the title.
title_offset_x	A numeric value to shift the title along the x-axis.
title_offset_y	A numeric value to shift the title along the y-axis.
title_hjust	The horizontal justification for the title: e.g. 0 (left aligned); 0.5 (centered); 1 (right aligned).
cluster_column	A logical scalar, specifying whether columns of the heatmap should be clustered by similarity. This is ignored when column_order is given.
dist_method	See method in dist. The distance method used for clustering columns.
hclust_method	See method in hclust. The clustering method used for clustering columns.
show_row_tree	A logical scalar (default TRUE). If FALSE, the figure provided in tree_fig is not shown.

Value

A ggtree object.

Author(s)

Ruizhu Huang

Examples

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

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

## Prepare the tree figure
tree_fig <- ggtree(rowTree(tse), branch.length = "none",
                   layout = "rectangular") +
    geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
    geom_hilight(node = 13, fill = "blue", alpha = 0.3)
tree_fig

## Simple heatmap with tree
TreeHeatmap(tree = rowTree(tse), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tse, "counts"))

## 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)))))

## Visualize aggregated heatmap with tree
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"))

## Cluster columns
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE)

## Split columns
col_split <- ifelse(colnames(tseagg) %in% paste0("S", seq_len(5)), "A", "B")
names(col_split) <- colnames(tseagg)
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE, column_split = col_split)

## Annotate columns
col_anno <- col_split
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE, column_split = col_split,
            column_anno = col_anno, column_anno_gap = 1)

## Change annotation colors
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE, column_split = col_split,
            column_anno = col_anno, column_anno_gap = 1,
            column_anno_color = c(A = "red", B = "blue"))

## Add column names
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE, column_split = col_split,
            column_anno = col_anno, column_anno_gap = 1,
            column_anno_color = c(A = "red", B = "blue"),
            show_colnames = TRUE, colnames_position = "bottom",
            colnames_angle = 90, colnames_size = 2,
            colnames_offset_y = -0.4)

## Add title
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE, column_split = col_split,
            column_anno = col_anno, column_anno_gap = 1,
            column_anno_color = c(A = "red", B = "blue"),
            show_colnames = TRUE, colnames_position = "bottom",
            colnames_angle = 90, colnames_size = 2,
            colnames_offset_y = -0.4,
            show_title = TRUE, title_offset_y = 2,
            title_color = "blue")

## Change colors
TreeHeatmap(tree = rowTree(tseagg), tree_fig = tree_fig,
            hm_data = SummarizedExperiment::assay(tseagg, "counts"),
            cluster_column = TRUE, column_split = col_split,
            column_anno = col_anno, column_anno_gap = 1,
            column_anno_color = c(A = "red", B = "blue"),
            show_colnames = TRUE, colnames_position = "bottom",
            colnames_angle = 90, colnames_size = 2,
            colnames_offset_y = -0.4,
            show_title = TRUE, title_offset_y = 2,
            title_color = "blue") +
            scale_fill_gradientn(
                colours = c("blue", "yellow", "red"),
                values = scales::rescale(c(5, 8, 10)),
                guide = "colorbar", limits = c(5, 10))

fionarhuang/treeclimbR documentation built on May 19, 2024, 1:18 p.m.