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Arrange Plots in a Heatmap

Source: R/layout-heatmap-.R
heatmap_layout.Rd

[Stable]

heatmap_layout is a specialized version of quad_alignb(), which simplifies the creation of heatmap plots by integrating essential elements for a standard heatmap layout, ensuring that the appropriate data mapping and visualization layers are automatically applied. ggheatmap is an alias for heatmap_layout.

Usage

heatmap_layout(
  data = NULL,
  mapping = aes(),
  ...,
  width = NA,
  height = NA,
  filling = waiver(),
  theme = NULL,
  active = NULL,
  set_context = deprecated(),
  order = deprecated(),
  name = deprecated(),
  guides = deprecated()
)

Arguments

data

Default dataset to use for the layout. If not specified, it must be supplied in each plot added to the layout. By default, it will try to inherit from parent layout. If not already a matrix, will be converted to one by fortify_matrix().

mapping

Default list of aesthetic mappings to use for plot. If not specified, must be supplied in each layer added to the plot.

...

Additional arguments passed to fortify_matrix().

width, height

The relative width/height of the main plot, can be a unit object.

filling

A single string of "raster" or "tile" to indicate the filling style. By default, waiver() is used, which means that if the input matrix has more than 20,000 cells (nrow * ncol > 20000), geom_raster() will be used for performance efficiency; for smaller matrices, geom_tile() will be used. To customize the filling style, set this to NULL.

For backward compatibility, a single boolean value is acceptable: TRUE means waiver(), and FALSE means NULL.

By default, the classic heatmap color scheme scale_fill_gradient2(low = "blue", high = "red") is utilized for continuous values.

You can use the options "ggalign.heatmap_continuous_fill" or "ggalign.heatmap_discrete_fill" to modify the default heatmap body filling color scale. See scale_fill_continuous() or scale_fill_discrete() for details on option settings.

theme

A theme() used to render the guides, title, subtitle, caption, margins, patch.title, panel.border, and background. If NULL (default), will inherit from the parent layout.

active

A active() object that defines the context settings when added to a layout.

set_context

[Deprecated] Please use active argument instead.

order

[Deprecated] Please use active argument instead.

name

[Deprecated] Please use active argument instead.

guides

[Deprecated] Please use plot_align() function instead.

Value

A HeatmapLayout object.

ggplot2 specification

The data input in ggheatmap will be converted into the long formated data frame when drawing. The default mapping will use aes(.data$.x, .data$.y), you can use mapping argument to control it. The data in the underlying ggplot object contains following columns:

  • .xpanel and .ypanel: the column and row panel

  • .x and .y: the x and y coordinates

  • .row_names and .column_names: A factor of the row and column names of the original matrix (only applicable when names exist).

  • .row_index and .column_index: the row and column index of the original matrix.

  • value: the actual matrix value.

Examples

ggheatmap(1:10)
#> → heatmap built with `geom_tile()`

ggheatmap(letters)
#> → heatmap built with `geom_tile()`

ggheatmap(matrix(rnorm(81), nrow = 9L))
#> → heatmap built with `geom_tile()`