tof_plot_heatmap: Make a heatmap summarizing group marker expression patterns...

In keyes-timothy/tidytof: Analyze High-dimensional Cytometry Data Using Tidy Data Principles

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

Description

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.

keyes-timothy/tidytof documentation built on Aug. 28, 2024, 8:37 a.m.