tof_plot_cells_density: Plot marker expression density plots

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

Plot marker expression density plots

Description

This function plots marker expression density plots for a user-specified column in a tof_tbl. Optionally, cells can be grouped to plot multiple vertically-arranged density plots

Usage

tof_plot_cells_density(
  tof_tibble,
  marker_col,
  group_col,
  num_points = 512,
  theme = ggplot2::theme_bw(),
  use_ggridges = FALSE,
  scale = 1,
  ...
)

Arguments

tof_tibble	A 'tof_tbl' or a 'tibble'.
marker_col	An unquoted column name representing which column in 'tof_tibble' (i.e. which CyTOF protein measurement) should be included in the feature extraction calculation.
group_col	Unquoted column names representing which column in 'tof_tibble' should be used to break the rows of 'tof_tibble' into subgroups to be plotted as separate histograms. Defaults to plotting without subgroups.
num_points	The number of points along the full range of 'marker_col' at which the density should be calculated
theme	The ggplot2 theme for the plot. Defaults to theme_bw
use_ggridges	A boolean value indicting if geom_ridgeline should be used to plot overlain histograms. Defaults to FALSE. If TRUE, the ggridges package must be installed.
scale	Use to set the 'scale' argument in geom_ridgeline, which controls how far apart (vertically) density plots are arranged along the y-axis. Defaults to 1.
...	Additional optional arguments to send to geom_ridgeline.

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(c("a", "b"), size = 1000, replace = TRUE)
    )

density_plot <-
    tof_plot_cells_density(
        tof_tibble = sim_data,
        marker_col = cd45,
        group_col = cluster_id
    )

keyes-timothy/tidytof documentation built on May 7, 2024, 12:33 p.m.