Workaround for Plotting Dendrograms
code
beginner
r
dendrograms
I think I have a solution to get decent enough dendrograms without fussing with base graphics.
The overview of my workaround is to cluster with pvclust, extract $hclust , plot it as a dendrogram, coerce into a ggplot. This makes it easy enough to replicate the functionality of the colored_bars() function by making additional plots. The function below makes a few plots in addition to the dendrogram. If you end up working with base graphics anyway, dendextend is still worth a look.
Here’s an example:
# needed
library(pvclust)
library(tidyverse)
library(dendextend) # for color_labels
library(ggnewscale) # to accommodate two fill scales https://github.com/eliocamp/ggnewscale
# recommended
# install.packages("palmerpenguins")
library(palmerpenguins)
library(patchwork)
library(scales) # for overiding scientific notation on dendrogram y axis
# Make a demo dataset
tux <- select(palmerpenguins::penguins,
species,
bill_length_mm, bill_depth_mm,
flipper_length_mm, body_mass_g)
tux <- tux[complete.cases(tux), ]
set.seed(54646)
tux <- tux[sample(1:nrow(tux), 30), ] # for faster demo clustering
# Example use
o <-
mk_hclust_plts(
df = mutate(tux, uid = paste(seq(1, nrow(tux)), species, sep = "-")),
cluster_by = c("bill_length_mm", "bill_depth_mm",
"flipper_length_mm", "body_mass_g"),
uid_col = "uid",
n_clusters = 3,
true_groups = "species",
true_colors = RColorBrewer::brewer.pal(3, "Set2"),
cluster_colors = RColorBrewer::brewer.pal(3, "Set1")
)
# Patchwork to arrange the output plots
(o$dendrogram_both+
scale_y_continuous(limits = c(-.0001, 0.00022), labels = scales::comma)
)/
(o$group_compare_tile+
# lims(y = c(2, -2))+ # y axis can be flipped like so
theme(legend.position = "")
) /
(o$heatmap_raw + theme(legend.position = "right")) /
(o$heatmap_z + theme(legend.position = "right")) +
patchwork::plot_layout(heights = c(5, .3, 1.25, 1.25))
# example 2
# o <-
# mk_hclust_plts(
# df = mutate(iris, uid = paste(seq(1, nrow(iris)), Species, sep = "-")),
# cluster_by = c("Sepal.Length", "Sepal.Width", "Petal.Length", "Petal.Width"),
# uid_col = "uid",
# n_clusters = 3,
# true_groups = "Species",
# true_colors = RColorBrewer::brewer.pal(3, "Set2"),
# cluster_colors = RColorBrewer::brewer.pal(3, "Set1")
# )ps, it’s worth checking your code on sample datasets (penguins,iris, mpg, etc. ). That’ll help iron out weird behavior sooner rather than later. .png)
(2021-2-21) Edit: The original function here depended on the factor levels of the clusters and true groups to make the color’s consistent between plots (e.g. factors ordered abcdABCD not aAbBcCdD). This breaks down with some cases (e.g. if you start group names with a number (e.g. 0hours)). The below edit uses ggnewscale to fix this.
mk_hclust_plts <- function(
df = unite(M_winxiqr, uid, Experiment, Cell, sep = "-"),
cluster_by = c("vrest", "r11", "r1", "Ihtk.0", "Ihtk.Slope", "Ia.0", "Ia.Slope"),
uid_col = "uid",
n_clusters = 3,
true_groups = "Condition",
true_colors = RColorBrewer::brewer.pal(3, "Set2"),
cluster_colors = RColorBrewer::brewer.pal(3, "Set1")
){
df <- as.data.frame(df)
if (!exists("cluster_colors")){
cluster_colors = rainbow(n_clusters)
}
## prep
# move uid to rowname
row.names(df) <- df[[uid_col]]
df_groups <- select(df, all_of(true_groups))
df <- df[, cluster_by]
## Cluster
cluster <- pvclust(t(df),
method.hclust = "ward.D2",
method.dist = "correlation",
use.cor = "pairwise.complete.obs")
## make dendrogram ####
dend <- cluster$hclust %>%
as.dendrogram()
# iteratively coloring the labels is a workaround to get the "true" groups shown
dend_labs <- rownames_to_column(df_groups, var = "rownames")[, ]
dend_labs <- full_join(data.frame(rownames = labels(dend)), dend_labs)
for(i in seq_along(unique(df_groups[[true_groups]]))){
true_group <- unique(df_groups[[true_groups]])[i]
true_color <- true_colors[i]
dend <- dend %>%
dendextend::color_labels(
col = true_color,
labels = dend_labs[dend_labs[[true_groups]] == true_group, "rownames"])
}
dend <- dend %>%
set("branches_k_color",
k = n_clusters,
value = cluster_colors
) %>%
set("branches_lwd", 0.7) %>%
set("labels_cex", 0.6)
dend_cluster_only <- dend %>%
set("labels_colors",
k = n_clusters,
value = cluster_colors) %>%
as.ggdend()
dend <- dend %>%
as.ggdend()
plt_dend_cluster_only <- ggplot(dend_cluster_only)+
theme(axis.ticks.y = element_line(),
axis.text.y = element_text(),
axis.line.y = element_line())
plt_dend <- ggplot(dend)+
theme(axis.ticks.y = element_line(),
axis.text.y = element_text(),
axis.line.y = element_line())
## Add reality ribbon with or without clustering result ####
groups_to_plt <- full_join(
as.data.frame(dend$labels),
rownames_to_column(var = "label", df_groups))
plt_grouping <- groups_to_plt %>%
ggplot(aes_string(x="x", y="0", fill = true_groups))+
geom_tile()+
scale_fill_manual(values = true_colors)+
theme_void()+
labs(x = "", y = "")+
theme(legend.position = "left")
plt_grouping_contrast <- ggplot()+
geom_tile(data = groups_to_plt, aes_string(x="x", y="0.5", fill = true_groups))+
scale_fill_manual(values = true_colors)+
ggnewscale::new_scale("fill") +
geom_tile(data = data.frame(x = seq_along(dend_cluster_only$labels$col),
cluster_groups = as.character(as.numeric(as.factor(dend_cluster_only$labels$col)))
),
aes_string(x="x", y= "-0.5", fill = "cluster_groups"),
)+
scale_fill_manual(values = cluster_colors)+
theme_void()+
labs(x = "", y = "")+
theme(legend.position = "left")
## Add heatmap ####
data_to_plt <- full_join(
as.data.frame(dend$labels),
rownames_to_column(var = "label", df))
data_to_plt <-
data_to_plt %>%
gather("key", "value",
names(data_to_plt)[
!(names(data_to_plt) %in% c("x", "y",
"label", "col", "cex",
true_groups))
])
plt_heatmap_raw <- data_to_plt %>%
ggplot(aes(x,
y = key,
fill = value))+
geom_tile()+
scale_fill_viridis_c()+
labs(x = "", y = "")+
theme(panel.background = element_blank(),
axis.ticks.x = element_blank(),
axis.text.x = element_blank(),
legend.position = "left")
plt_heatmap_z <- data_to_plt %>%
group_by(key) %>%
mutate(mean = mean(value, na.rm = T),
sd = sd(value, na.rm = T)) %>%
mutate(value = ((value - mean)/sd)) %>% # Now Z scores
ggplot(aes(x,
y = key,
fill = value))+
geom_tile()+
scale_fill_viridis_c()+
labs(x = "", y = "")+
theme(panel.background = element_blank(),
axis.ticks.x = element_blank(),
axis.text.x = element_blank(),
legend.position = "left")
## Return plots, manually tweak layout ####
return(
list(
pvclust_out = cluster,
dendrogram_clusters = plt_dend_cluster_only,
dendrogram_both = plt_dend,
group_tile = plt_grouping,
group_compare_tile = plt_grouping_contrast,
heatmap_raw = plt_heatmap_raw,
heatmap_z = plt_heatmap_z
)
)
}