heat_map: No-frills heatmap
In m20ty/matkot: Make Matrices Fun!

View source: R/heat_map.R

heat_map

R Documentation

No-frills heatmap

Description

Makes a heatmap with optional row/column ordering and aligned dendrograms.

Usage

heat_map(
  mat,
  ord = NULL,
  ord_x = NULL,
  ord_y = NULL,
  draw_dendro = FALSE,
  return_data = FALSE,
  show_legend = TRUE,
  plot_title = NULL,
  axis_text_x = colnames(mat),
  axis_text_y = rownames(mat),
  axis_title_x = waiver(),
  axis_title_y = waiver(),
  colours = c("red", "yellow"),
  limits = NULL,
  oob = scales::squish,
  legend_breaks = waiver(),
  legend_labels = waiver(),
  legend_title = waiver(),
  axis_ticks = element_blank(),
  axis_ticks_length = 0,
  axis_text_size = 7,
  plot_margin = c(5.5, 5.5, 5.5, 5.5),
  rel_widths = c(heatmap = 1, dend = 0.2, legend = 0.2),
  rel_heights = c(heatmap = 1, dend = 0.2),
  ...
)

Arguments

`mat`	A numeric matrix.
`ord`	An optional ordering object with which to reorder both the rows and the columns of `mat`. Can be an `hclust` object or an integer permutation vector.
`ord_x`	An optional ordering object with which to reorder the columns of `mat`. Can be an `hclust` object or an integer permutation vector. Ignored if `ord` is supplied.
`ord_y`	An optional ordering object with which to reorder the rows of `mat`. Can be an `hclust` object or an integer permutation vector. Ignored if `ord` is supplied.
`draw_dendro`	Logical or character indicating whether to draw dendrograms or which dendrograms to draw. Possible values are `TRUE`, `FALSE`, 'x', 'y', 'xy'. If `TRUE` or 'xy', all possible dendrograms will be drawn. Default: `FALSE`.
`return_data`	Logical indicating whether to return a data frame (in long format) containing the data used to construct the heatmap.
`show_legend`	Logical indicating whether to show the heatmap legend.
`plot_title`	The title of the plot. Set to `NULL` if you don't want a title. Default: `NULL`.
`axis_text_x`	Character vector of x axis labels. These will be re-ordered if `ord` or `ord_x` are supplied. Set to `NULL` if you want no x axis labels. Default: `colnames(mat)`.
`axis_text_y`	Character vector of y axis labels. These will be re-ordered if `ord` or `ord_y` are supplied. Set to `NULL` if you want no y axis labels. Default: `rownames(mat)`.
`axis_title_x`	The x axis title. Set to `NULL` if you want no x axis title.
`axis_title_y`	The y axis title. Set to `NULL` if you want no y axis title.
`colours`	The colours to be used in the heatmap. These will be converted to a colour scale by ggplot2's `scale_fill_gradientn`. Default: c('red', 'yellow').
`limits`	Two-element numeric vector specifying the limits to use for the colour scale.
`oob`	A function to handle values lying outside the range specified by `limits`. Default: `scales::squish`.
`legend_breaks`	A numeric vector of legend breaks.
`legend_labels`	A vector of legend labels.
`legend_title`	The legend title. Set to `NULL` if you want no legend title.
`axis_ticks`	As `axis.ticks` in `theme`.
`axis_ticks_length`	As `axis.ticks.length` in `theme`.
`axis_text_size`	The size of the axis text. Default: 7.
`plot_margin`	Numeric vector of plot margins in pts, in the order top, right, bottom, left. Default: c(5.5, 5.5, 5.5, 5.5).
`rel_widths`	Named vector of relative widths to be passed to cowplot's `plot_grid`. Names should include 'heatmap' and, if applicable, 'dend' and 'legend'.
`rel_heights`	Named vector of relative heights to be passed to cowplot's `plot_grid`. Names should include 'heatmap' and, if applicable, 'dend'.
`...`	Additional arguments to be passed to ggplot2's `theme` function in the construction of the heatmap.

Value

If return_data is FALSE, a ggplot object. If return_data is TRUE, a list with two elements: plot, a ggplot object; and data, a data frame.