tof_plot_clusters_heatmap: Make a heatmap summarizing cluster marker expression patterns...

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

Make a heatmap summarizing cluster marker expression patterns in CyTOF data

Description

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

Usage

tof_plot_clusters_heatmap(
  tof_tibble,
  cluster_col,
  marker_cols = where(tof_is_numeric),
  central_tendency_function = stats::median,
  scale_markerwise = FALSE,
  scale_clusterwise = FALSE,
  cluster_markers = TRUE,
  cluster_clusters = TRUE,
  line_width = 0.25,
  theme = ggplot2::theme_minimal()
)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
cluster_col	An unquoted column name indicating which column in 'tof_tibble' stores the cluster ids for the cluster to which each cell belongs. Cluster labels can be produced via any method the user chooses - including manual gating, any of the functions in the 'tof_cluster_*' function family, or any other method.
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_clusterwise	A boolean value indicating if the heatmap should rescale the rows of the heatmap such that the maximum value for each cluster 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_clusters	A boolean value indicating if the heatmap should order its rows (i.e. clusters) 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.

Examples

sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = rnorm(n = 1000),
        cd34 = rnorm(n = 1000),
        cd19 = rnorm(n = 1000),
        cluster_id = sample(letters, size = 1000, replace = TRUE)
    )

heatmap <-
    tof_plot_clusters_heatmap(
        tof_tibble = sim_data,
        cluster_col = cluster_id
    )

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