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Make a heatmap summarizing group marker expression patterns in high-dimensional cytometry data

Source: R/utils.R
tof_plot_heatmap.Rd

This function makes a heatmap of group-to-group marker expression patterns in single-cell data. Markers are plotted along the horizontal (x-) axis of the heatmap and groups are plotted along the vertical (y-) axis of the heatmap.

Usage

tof_plot_heatmap(
  tof_tibble,
  y_col,
  marker_cols = where(tof_is_numeric),
  central_tendency_function = stats::median,
  scale_markerwise = FALSE,
  scale_ywise = FALSE,
  cluster_markers = TRUE,
  cluster_groups = TRUE,
  line_width = 0.25,
  theme = ggplot2::theme_minimal()
)

Arguments

tof_tibble

A `tof_tbl` or a `tibble`.

y_col

An unquoted column name indicating which column in `tof_tibble` stores the ids for the group to which each cell belongs.

marker_cols

Unquoted column names indicating which column in `tof_tibble` should be interpreted as markers to be plotted along the x-axis of the heatmap. Supports tidyselect helpers.

central_tendency_function

A function to use for computing the measure of central tendency that will be aggregated from each cluster in cluster_col. Defaults to the median.

scale_markerwise

A boolean value indicating if the heatmap should rescale the columns of the heatmap such that the maximum value for each marker is 1 and the minimum value is 0. Defaults to FALSE.

scale_ywise

A boolean value indicating if the heatmap should rescale the rows of the heatmap such that the maximum value for each group is 1 and the minimum value is 0. Defaults to FALSE.

cluster_markers

A boolean value indicating if the heatmap should order its columns (i.e. markers) using hierarchical clustering. Defaults to TRUE.

cluster_groups

A boolean value indicating if the heatmap should order its rows (i.e. groups) using hierarchical clustering. Defaults to TRUE.

line_width

A numeric value indicating how thick the lines separating the tiles of the heatmap should be. Defaults to 0.25.

theme

A ggplot2 theme to apply to the heatmap. Defaults to theme_minimal

Value

A ggplot object.