Color side bar dendrogram plot

问题

Initially I was trying to add the horizontal color side bar to the dendrogram plot (NOT to the whole heat map) using colored_bars from dendextend.

The code below (THANK YOU for your help Tal!) works pretty well. The only issue remaining is how to control the distance of the bar from the leaves labels and the bar width?

Here is an example, data and code
Data (4 variables, 5 cases)

df <- read.table(header=T, text="group class v1 v2 
1          A         1          3.98         23.2  
2          A         2          5.37         18.5  
3          C         1          4.73         22.1  
4          B         1          4.17         22.3  
5          C         2          4.47         22.4  
") 

car_type <- factor(df[,c(1)]) # groups codes (A,B,C)  
cols_4 <- heat.colors(3)  
col_car_type <- cols_4[car_type] 
matrix<-data.matrix(df[,c(3,4)])
rnames<-df[,2]
row.names(matrix)<-rnames
matrix<-data.matrix(df[,c(3,4)])
row.names(matrix)<-rnames
dend<-hclust(dist(matrix))
labels_colors(dend) <- col_car_type[order.dendrogram(dend)]  # Error in order.dendrogram(dend) : 'order.dendrogram' requires a dendrogram
# But I dont think the line above is doing anything so it can be removed...
plot(dend)  
colored_bars(col_car_type, dend)

回答1:

This is now possible to do using dendextend version 1.1.4 (currently available on github, and will also be on CRAN in the next month or so).

First to install the latest dendextend version you can use:

install.packages.2 <- function (pkg) if (!require(pkg)) install.packages(pkg);
install.packages.2('devtools')
devtools::install_github('talgalili/dendextend')

Here is an example using mtcars:

## mtcars example

# Create the dend:
dend <- as.dendrogram(hclust(dist(mtcars)))

# Create a vector giving a color for each car to which company it belongs to
car_type <- rep("Other", length(rownames(mtcars)))
is_x <- grepl("Merc", rownames(mtcars))
car_type[is_x] <- "Mercedes"
is_x <- grepl("Mazda", rownames(mtcars))
car_type[is_x] <- "Mazda"
is_x <- grepl("Toyota", rownames(mtcars))
car_type[is_x] <- "Toyota"
car_type <- factor(car_type)
n_car_types <- length(unique(car_type))
cols_4 <- colorspace::rainbow_hcl(n_car_types, c = 70, l  = 50)
col_car_type <- cols_4[car_type]

# extra: showing the various clusters cuts 
k234 <- cutree(dend, k = 2:4)

# color labels by car company:
labels_colors(dend) <- col_car_type[order.dendrogram(dend)]
# color branches based on cutting the tree into 4 clusters:
dend <- color_branches(dend, k = 4)

### plots
par(mar = c(12,4,1,1))
plot(dend)
colored_bars(cbind(k234[,3:1], col_car_type), dend, rowLabels = c(paste0("k = ", 4:2), "Car Type"))

# horiz version:
par(mar = c(4,1,1,12))
plot(dend, horiz = TRUE)
colored_bars(cbind(k234[,3:1], col_car_type), dend, rowLabels = c(paste0("k = ", 4:2), "Car Type"), horiz = TRUE)
legend("topleft", legend = levels(car_type), fill = cols_4)

来源：https://stackoverflow.com/questions/34539746/color-side-bar-dendrogram-plot

标签

dendrogram

dendextend