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Plot scatterplots of single-cell data using low-dimensional feature embeddings

Source: R/visualization.R
tof_plot_cells_embedding.Rd

This function makes scatterplots using single-cell data embedded in a low-dimensional space (such as that generated by tof_reduce_dimensions, with each point colored using a user-specified variable.

Usage

tof_plot_cells_embedding(
  tof_tibble,
  embedding_cols,
  color_col,
  facet_cols,
  compute_embedding_cols = where(tof_is_numeric),
  embedding_method = c("pca", "tsne", "umap"),
  embedding_args = list(),
  theme = ggplot2::theme_bw(),
  ...,
  method = c("ggplot2", "scattermore")
)

Arguments

tof_tibble

A `tof_tbl` or a `tibble`.

embedding_cols

Unquoted column names indicating which columns in `tof_tibble` should be used as the x and y axes of the scatterplot. Supports tidyselect helpers. Must select exactly 2 columns. If not provided, a feature embedding can be computed from scratch using the method provided using the `embedding_method` argument and the tof_reduce_dimensions arguments passed to `embedding_args`.

color_col

An unquoted column name specifying which column in `tof_tibble` should be used to color each point in the scatterplot.

facet_cols

An unquoted column name specifying which column in `tof_tibble` should be used to break the scatterplot into facets using facet_wrap.

compute_embedding_cols

Unquoted column names indicating which columns in 'tof_tibble' to use for computing the embeddings with the method specified by `embedding_method`. Defaults to all numeric columns in 'tof_tibble'. Supports tidyselect helpers.

embedding_method

A string indicating which method should be used for the feature embedding (if `embedding_cols` are not provided). Options (which are passed to tof_reduce_dimensions) are "pca" (the default), "tsne", and "umap".

embedding_args

Optional additional arguments to pass to tof_reduce_dimensions. For example, for `method = "tsne"`, these might include `num_comp`, `perplexity`, and `theta`.

theme

A ggplot2 theme to apply to the scatterplot. Defaults to theme_bw.

...

Optional additional arguments to pass to tof_plot_cells_scatter.

method

A string indicating which plotting engine should be used. Valid values include "ggplot2" (the default) and "scattermore" (recommended if more than 100K cells are being plotted). Note that method = "scattermore" requires the scattermore package to be installed.

Value

A ggplot object.

See also

Other visualization functions: tof_plot_cells_layout(), tof_plot_cells_scatter()

Examples


sim_data <-
    dplyr::tibble(
        cd45 = rnorm(n = 1000),
        cd38 = c(rnorm(n = 500), rnorm(n = 500, mean = 2)),
        cd34 = c(rnorm(n = 500), rnorm(n = 500, mean = 4)),
        cd19 = rnorm(n = 1000),
        cluster_id = c(rep("a", 500), rep("b", 500))
    )

# embed with pca
pca_plot <-
    tof_plot_cells_embedding(
        tof_tibble = sim_data,
        color_col = cd38,
        embedding_method = "pca",
        compute_embedding_cols = starts_with("cd")
    )

# embed with tsne
tsne_plot <-
    tof_plot_cells_embedding(
        tof_tibble = sim_data,
        color_col = cluster_id,
        embedding_method = "tsne",
        compute_embedding_cols = starts_with("cd")
    )