tof_plot_cells_layout: Plot force-directed layouts of single-cell data

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

Plot force-directed layouts of single-cell data

Description

This function makes force-directed layouts using single-cell data embedded in a 2-dimensional space representing a k-nearest-neighbor graph constructed using cell-to-cell similarities. Each node in the force-directed layout represents a single cell colored using a user-specified variable.

Usage

tof_plot_cells_layout(
  tof_tibble,
  knn_cols = where(tof_is_numeric),
  color_col,
  facet_cols,
  num_neighbors = 5,
  graph_type = c("weighted", "unweighted"),
  graph_layout = "fr",
  distance_function = c("euclidean", "cosine"),
  edge_alpha = 0.25,
  node_size = 2,
  theme = ggplot2::theme_void(),
  ...
)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
knn_cols	Unquoted column names indicating which columns in 'tof_tibble' should be used to compute the cell-to-cell distances used to construct the k-nearest-neighbor graph. Supports tidyselect helpers. Defaults to all numeric columns.
color_col	Unquoted column name indicating which column in 'tof_tibble' should be used to color the nodes in the force-directed layout.
facet_cols	Unquoted column names indicating which columns in 'tof_tibble' should be used to separate nodes into different force-directed layouts.
num_neighbors	An integer specifying how many neighbors should be used to construct the k-nearest neighbor graph.
graph_type	A string specifying if the k-nearest neighbor graph should be "weighted" (the default) or "unweighted".
graph_layout	A string specifying which algorithm should be used to compute the force-directed layout. Passed to ggraph. Defaults to "fr", the Fruchterman-Reingold algorithm. Other examples include "nicely", "gem", "kk", and many others. See layout_tbl_graph_igraph for other examples.
distance_function	A string indicating which distance function to use in computing the cell-to-cell distances. Valid options include "euclidean" (the default) and "cosine".
edge_alpha	A numeric value between 0 and 1 specifying the transparency of the edges drawn in the force-directed layout. Defaults to 0.25.
node_size	A numeric value specifying the size of the nodes in the force-directed layout. Defaults to 2.
theme	A ggplot2 theme to apply to the force-directed layout. Defaults to theme_void
...	hnsw_knn

Value

A ggraph/ggplot object.

See Also

Other visualization functions: tof_plot_cells_embedding(), 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))
    )

# make a layout colored by a marker
layout_cd38 <-
    tof_plot_cells_layout(
        tof_tibble = sim_data,
        color_col = cd38
    )

# make a layout colored by cluster id
layout_cluster <-
    tof_plot_cells_layout(
        tof_tibble = sim_data,
        color_col = cluster_id,
    )

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