decrease size of dendogram (or y-axis) ggplot

问题:

I have this code for a dendrogram. How can I decrease the size of dendrogram (or y-axis)?

I am using this code as example. In my dataset, I have large labels so I do not have space enough to include it. For that reason, I would like to reduce the space used for y axis, decrease the distance between 0 and 150. Also, when I save the figure as tiff, most of figure is the dendogram and I can not see labels clearly.

df   <- USArrests                 # really bad idea to muck up internal datasets
labs <- paste("sta_",1:50,sep="") # new labels
rownames(df) <- labs              # set new row names

library(ggplot2)
library(ggdendro)
hc       <- hclust(dist(df), "ave")           # heirarchal clustering
dendr    <- dendro_data(hc, type="rectangle") # convert for ggplot
clust    <- cutree(hc,k=2)                    # find 2 clusters
clust.df <- data.frame(label=names(clust), cluster=factor(clust))
# dendr[["labels"]] has the labels, merge with clust.df based on label column
dendr[["labels"]] <- merge(dendr[["labels"]],clust.df, by="label")
# plot the dendrogram; note use of color=cluster in geom_text(...)
ggplot() + 
  geom_segment(data=segment(dendr), aes(x=x, y=y, xend=xend, yend=yend)) + 
  geom_text(data=label(dendr), 
            aes(x, y, label=label, hjust=0, color=cluster), 
            size=3) +
  coord_flip() + 
  scale_y_reverse(expand=c(0.2, 0)) + 
  theme(axis.line.y=element_blank(),
        axis.ticks.y=element_blank(),
        axis.text.y=element_blank(),
        axis.title.y=element_blank(),
        panel.background=element_rect(fill="white"),
        panel.grid=element_blank())

How can I decrease the size of dendogram similar than this heatmap?

Thanks you so much

回答1:

For flexibility, I recommend putting the dendrogram labels on the x-axis itself, rather than text labels within the plot. Otherwise no matter what values you choose for expand in the y-axis, part of the labels could be cut off for some image sizes / dimensions.

Define colour palette for the dendrogram labels:

library(dplyr)
label.colour = label(dendr)$cluster %>% 
  factor(levels = levels(.),
         labels = scales::hue_pal()(n_distinct(.))) %>%
  as.character()

For the purpose of illustration, make some labels very long:

label.values <- forcats::fct_recode(
  label(dendr)$label,
  sta_45_abcdefghijklmnop = "sta_45",
  sta_31_merrychristmas = "sta_31",
  sta_6_9876543210 = "sta_6")

Plot:

p <- ggplot(segment(dendr)) + 
  geom_segment(aes(x=x, y=y, xend=xend, yend=yend)) +
  coord_flip() +
  scale_x_continuous(breaks = label(dendr)$x,

                     # I'm using label.values here because I made
                     # some long labels for illustration. you can
                     # simply use `labels = label(dendr)$label`
                     labels = label.values, 

                     position = "top") +
  scale_y_reverse(expand = c(0, 0)) +
  theme_minimal() +
  theme(axis.title = element_blank(),
        axis.text.y = element_text(size = rel(0.9),
                                   color = label.colour),
        panel.grid = element_blank())
p

# or if you want a color legend for the clusters
p + geom_point(data = label(dendr), 
               aes(x = x, y = y, color = cluster), alpha = 0) +
  scale_color_discrete(name = "Cluster",
                       guide = guide_legend(override.aes = list(alpha = 1))) +
  theme(legend.position = "bottom")

回答2:

You can do this by adding a size parameter to axis.text.y like so:

theme(axis.line.y=element_blank(),
    axis.ticks.y=element_blank(),

    axis.text.y=element_text(size=12),

    axis.title.y=element_blank(),
    panel.background=element_rect(fill="white"),
    panel.grid=element_blank())