getData: extract data used in the figure

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

Description

getData extracts data used to plot different elements in the figure, such as the heatmap, the row (column) names of the heatmap, etc.

Usage

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

Arguments

tree_hm	the output of TreeHeatmap.
type	It's chosen from "heatmap", "row_name", "column_name", "title", "column_anno", "column_order".

Author(s)

Ruizhu Huang

Examples

library(TreeSummarizedExperiment)
library(ggtree)
library(ggplot2)
library(ggnewscale)
library(viridis)
library(dplyr)

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))


col_split <- ifelse(colnames(ct) %in% paste0("S", 1:5),
                    "A", "B")
names(col_split) <- colnames(ct)
# 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)
 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

df_hm <- getData(tree_hm = fig, type = "heatmap")

ct <- df_hm %>%
    dplyr::select(x, width, variable) %>%
    distinct()

# generate data to do column annotation
set.seed(1)
ann <- matrix(sample(LETTERS[1:2], size = 3 * ncol(df_hm),
                     replace = TRUE),
              nrow = 3)
rownames(ann) <- paste0("g", 1:3)
colnames(ann) <- ct$variable
ann <- data.frame(ann) %>%
       mutate(y = min(df_hm$y) - seq_len(nrow(ann)),
       label = rownames(ann))
df_ann <- tidyr::gather(ann, variable, value, -c(y, label)) %>%
    left_join(ct)

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