TreeHeatmap: Heatmap at arbitary levels of a tree

In fionarhuang/TreeHeatmap_old: Display heatmap at different resolution level of a tree

Description

TreeHeatmap displays a heatmap at a arbitary 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,
  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 that outputs from ggtree.
hm_data	A data frame. Data to plot heatmap. Its rownames should be able to match to nodes of the tree.
tree_hm_gap	A numeric value to specify the gap between the tree and the heatmap.
rel_width	A numeric value to specify the width of heatmap relative to the width of the tree. For example, rel_width = 1, the width of heatmap is the same as the width of the tree.
cell_line_color	A color for the lines among cells of the heatmap. The default is NA.
cell_line_size	A value to specify the size of lines among cells of the heatmap. The default is 0.
column_order	A character vector that includes the column name of hm_data to specify the display order of the heatmap. It's ignored when column_split is provided.
column_split	A named character vector that gives the group information about columns to split the heatmap. It's named by the colnames of hm_data.
column_split_gap	A numeric value to specify the gap between the columns of heatmap that are split.
column_split_label	A named character vector to label the column split. It's named by the value or level of the column_split.
split_label_fontface	The fontface of the labels of the column split. The default is "bold".
split_label_color	The color of the the labels of the column split. The default is "black".
split_label_size	The size of the the labels of the column split. The default is 3.
split_label_angle	The angle of the the labels of the column split. The default is 0.
split_label_offset_x	A numeric value to shift the labels of the column split along x-axis. The defaut is 0.
split_label_offset_y	A numeric value to shift the labels of the column split along y-axis. The defaut is 2.
split_label_hjust	The hjust for the labels of the column split: 0 (left aligned); 0.5 (centered); 1 (right aligned). The default is 0.5
column_anno	A named vector to specify labels that are used to annotate 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 columns of 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. The default is FALSE.
colnames_position	The position of column names, "top" or "bottom".
colnames_angle	A numeric value. The angle of column names.
colnames_offset_x	A numeric value to shift column names on x-axis. The defaut is 0.
colnames_offset_y	A numeric value to shift column names on y-axis. The defaut is 0.
colnames_size	A numeric value to specify the size of column names.
colnames_hjust	The hjust for column names: 0 (left aligned); 0.5 (centered); 1 (right aligned).
show_rownames	A logical value to specify whether row names should be displayed. The default is FALSE.
rownames_position	"right" or "left".
rownames_angle	A numeric value. The angle of row names.
rownames_offset_x	A numeric value to shift row names on x-axis. The defaut is 0.
rownames_offset_y	A numeric value to shift row names on y-axis. The defaut is 0.
rownames_size	A numeric value to specify the size of row names.
rownames_hjust	The hjust for row names: 0 (left aligned); 0.5 (centered); 1 (right aligned).
rownames_label	A named vector to annotate the rows of heatmap instead the row names of hm_data.
show_title	A logical value to specify whether the title should be displayed. The default is FALSE.
title_hm	The title of heatmap
title_fontface	The fontface of the title. The default is "bold".
title_color	The color of the title. The default is "black".
title_size	The size of the title. The default is 3.
title_angle	The angle of the title. The default is 0.
title_offset_x	A numeric value to shift title along x-axis. The defaut is 0.
title_offset_y	A numeric value to shift title along y-axis. The defaut is 2.
title_hjust	The hjust for title: 0 (left aligned); 0.5 (centered); 1 (right aligned). The default is 0.5
cluster_column	A logical value, TRUE or FALSE. It specifies whether columns of the heatmap should be ordered by similarity. The default is TRUE. This is ignored when column_order is given.
dist_method	See method in dist. The distance method used in clustering columns. The default is "euclidean".
hclust_method	See method in hclust. The clustering method used in clustering columns. The default is "ave".
show_row_tree	TRUE or FALSE. Default is TRUE. If FALSE, the figure provied in tree_fig wouldn't be shown.

Author(s)

Ruizhu Huang

Examples

library(TreeSummarizedExperiment)
library(ggtree)
library(ggplot2)
library(scales)

data(tinyTree)

p1 <- c(rep(0.1/3, 3), rep(0.4/2, 2), rep(0.1, 5))
p2 <- c(rep(0.4/3, 3), rep(0.1/2, 2), rep(0.1, 5))
set.seed(1)
ct0 <- cbind(rmultinom(n = 5, size = 50, prob = p1),
             rmultinom(n = 5, size =50, prob = p2))
colnames(ct0) <- paste("S", 1:10, sep = "")
rownames(ct0) <- transNode(tree = tinyTree, node = 1:10)
oo <- sample(1:10)
ct0 <- ct0[, oo]

ct <- rbind(colSums(ct0[1:3, ]),
            colSums(ct0[4:5, ]),
            ct0[6:10, ])
colnames(ct) <- paste("S", 1:10, sep = "")
rownames(ct) <- transNode(tree = tinyTree, node = c(13, 18, 6:10))



# prepare the tree figure
tree_fig <- ggtree(tinyTree,
                   branch.length = "none",
                   layout = "rectangular", open.angle = 100) +
    #geom_text2(aes(label = label)) +
    geom_hilight(node = 18, fill = "orange", alpha = 0.3) +
    geom_hilight(node = 13, fill = "blue", alpha = 0.3)

# figure 0
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig, hm_data = ct0[, oo])

# figure 1
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig, hm_data = ct)

# figure 2: order column by similarity
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig,
            hm_data = ct, cluster_column = TRUE)

 # figure 3: split columns
col_split <- ifelse(colnames(ct) %in% paste0("S", 1:5),
                    "A", "B")
names(col_split) <- colnames(ct)
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig,
            hm_data = ct, cluster_column = TRUE,
            column_split = col_split)
# figure 4: annotate columns
col_anno <- col_split
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig,
            hm_data = ct, cluster_column = TRUE,
            column_split = col_split,
            column_anno = col_anno,
            column_anno_gap = 0.5)
# figure 5: change annotation colors
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig,
            hm_data = ct, cluster_column = TRUE,
            column_split = col_split,
            column_anno = col_anno,
            column_anno_gap = 0.6,
            column_anno_color = c("A" = "red", "B"= "blue"))

# figure 6: add colnames
TreeHeatmap(tree = tinyTree, tree_fig = tree_fig,
            hm_data = ct, cluster_column = TRUE,
            column_split = col_split,
            column_anno = col_anno,
            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)

# figure 7: add title
 fig <- TreeHeatmap(tree = tinyTree, tree_fig = tree_fig,
            hm_data = ct, cluster_column = TRUE,
            column_split = col_split,
            column_anno = col_anno,
            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
# use expand_limits to display the missing part of row names
(fig <- fig + expand_limits(x = c(0, 15)))

# change colors
fig +
scale_fill_viridis_c(option = "D")

fig +
 scale_fill_gradientn(colours = c("blue","yellow","red"),
                      values = scales::rescale(c(5, 8, 10)),
                      guide = "colorbar", limits=c(5, 10))

fionarhuang/TreeHeatmap_old documentation built on Feb. 25, 2021, 2:59 p.m.