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Make a heatmap summarizing cluster marker expression patterns in CyTOF data

Source: R/visualization.R
tof_plot_clusters_heatmap.Rd

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
    )