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Dendrogram scales

Source: R/scale-dendro.R
scale_x_dendro.Rd

These are speciality scales for use with hierarchically clustered data. The scale automatically orders the limits according to the clustering result and comes with a dendrogram axis.

Usage

scale_x_dendro(
  clust,
  ...,
  expand = waiver(),
  guide = "axis_dendro",
  position = "bottom"
)

scale_y_dendro(
  clust,
  ...,
  expand = waiver(),
  guide = "axis_dendro",
  position = "left"
)

Arguments

clust

A data structure that can be coerced to an <hclust> object through as.hclust().

...

Arguments passed on to ggplot2::discrete_scale

aesthetics

The names of the aesthetics that this scale works with.

palette

A palette function that when called with a single integer argument (the number of levels in the scale) returns the values that they should take (e.g., scales::pal_hue()).

name

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

breaks

One of:

  • NULL for no breaks

  • waiver() for the default breaks (the scale limits)

  • A character vector of breaks

  • A function that takes the limits as input and returns breaks as output. Also accepts rlang lambda function notation.

labels

One of:

  • NULL for no labels

  • waiver() for the default labels computed by the transformation object

  • A character vector giving labels (must be same length as breaks)

  • An expression vector (must be the same length as breaks). See ?plotmath for details.

  • A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

na.translate

Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify na.translate = FALSE.

na.value

If na.translate = TRUE, what aesthetic value should the missing values be displayed as? Does not apply to position scales where NA is always placed at the far right.

drop

Should unused factor levels be omitted from the scale? The default, TRUE, uses the levels that appear in the data; FALSE includes the levels in the factor. Please note that to display every level in a legend, the layer should use show.legend = TRUE.

call

The call used to construct the scale for reporting messages.

super

The super class to use for the constructed scale

expand

For position scales, a vector of range expansion constants used to add some padding around the data to ensure that they are placed some distance away from the axes. Use the convenience function expansion() to generate the values for the expand argument. The defaults are to expand the scale by 5% on each side for continuous variables, and by 0.6 units on each side for discrete variables.

guide

A function used to create a guide or its name. See guides() for more information.

position

For position scales, The position of the axis. left or right for y axes, top or bottom for x axes.

Value

A <ScaleDiscretePosition> object that can be added to a plot.

Details

The scale limits are determined by the order and labels in the clust argument. While limits is not an argument in these scales, the breaks argument can still be used to selectively omit some breaks and the labels can be used for formatting purposes.

See also

guide_axis_dendro()

Examples

# Hierarchically cluster data, separately for rows and columns
car_clust <- hclust(dist(scale(mtcars)), "ave")
var_clust <- hclust(dist(scale(t(mtcars))), "ave")

long_mtcars <- data.frame(
  car = rownames(mtcars)[row(mtcars)],
  var = colnames(mtcars)[col(mtcars)],
  value = as.vector(scale(mtcars))
)

# A standard heatmap adorned with dendrograms
p <- ggplot(long_mtcars, aes(var, car, fill = value)) +
  geom_tile() +
  scale_x_dendro(var_clust) +
  scale_y_dendro(car_clust)
p


# Styling the dendrograms
p +
  guides(
    y = guide_axis_dendro(key_dendro(type = "triangle")),
    x = guide_axis_dendro(space = rel(5))
  ) +
  theme(
    axis.text.y.left = element_text(margin = margin(r = 3, l = 3)),
    axis.ticks.y = element_line("red"),
    axis.ticks.x = element_line(linetype = "dotted")
  )


# In polar coordinates, plus some formatting
p +
  coord_radial(
    theta = "y", inner.radius = 0.5,
    start = 0.25 * pi, end = 1.75 * pi
  ) +
  guides(
    theta = primitive_labels(angle = 90),
    theta.sec = primitive_segments("dendro", vanish = TRUE),
    r = guide_axis_dendro(angle = 0)
  )