Cell velocity plot

The plot shows the velocity vectors of the cells in a specified reduction space.

Usage

VelocityPlot(
  embedding,
  v_embedding,
  plot_type = c("raw", "grid", "stream"),
  split_by = NULL,
  group_by = NULL,
  group_name = "Group",
  group_palette = "Paired",
  group_palcolor = NULL,
  n_neighbors = NULL,
  density = 1,
  smooth = 0.5,
  scale = 1,
  min_mass = 1,
  cutoff_perc = 5,
  arrow_angle = 20,
  arrow_color = "black",
  arrow_alpha = 1,
  streamline_l = 5,
  streamline_minl = 1,
  streamline_res = 1,
  streamline_n = 15,
  streamline_width = c(0, 0.8),
  streamline_alpha = 1,
  streamline_color = NULL,
  streamline_palette = "RdYlBu",
  streamline_palcolor = NULL,
  streamline_bg_color = "white",
  streamline_bg_stroke = 0.5,
  aspect.ratio = 1,
  title = "Cell velocity",
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme = "theme_this",
  theme_args = list(),
  return_layer = FALSE,
  seed = 8525
)

Arguments

embedding: A matrix or data.frame of dimension n_obs x n_dim specifying the embedding coordinates of the cells.
v_embedding: A matrix or data.frame of dimension n_obs x n_dim specifying the velocity vectors of the cells.
plot_type: A character string specifying the type of plot to create. Options are "raw", "grid", or "stream". Default is "raw".
split_by: An optional character string specifying a variable to split the plot by. Not supported yet.
group_by: An optional character string specifying a variable to group the cells by.
group_name: An optional character string specifying the name of the grouping variable in legend. Default is "Group".
group_palette: A character string specifying the color palette to use for grouping. Default is "Paired".
group_palcolor: An optional character vector specifying the colors to use for grouping. If NULL, the colors will be generated from the group_palette.
n_neighbors: An optional numeric value specifying the number of nearest neighbors for each grid point. Default is ceiling(ncol(embedding) / 50).
density: An optional numeric value specifying the density of the grid points along each dimension. Default is 1.
smooth: An optional numeric value specifying the smoothing factor for the velocity vectors. Default is 0.5.
scale: An optional numeric value specifying the scaling factor for the velocity vectors. Default is 1.
min_mass: An optional numeric value specifying the minimum mass required for a grid point to be considered. Default is 1.
cutoff_perc: An optional numeric value specifying the percentile cutoff for removing low-density grid points. Default is 5.
arrow_angle: An optional numeric value specifying the angle of the arrowheads in degrees for velocity arrows. Default is 20.
arrow_color: A character string specifying the color of the velocity arrowheads. Default is "black".
arrow_alpha: A numeric value specifying the transparency of the velocity arrows. Default is 1 (fully opaque). Only works for plot_type = "raw" and plot_type = "grid". For plot_type = "stream", use streamline_alpha instead.
streamline_l: An optional numeric value specifying the length of the velocity streamlines. Default is 5.
streamline_minl: An optional numeric value specifying the minimum length of the velocity streamlines. Default is 1.
streamline_res: An optional numeric value specifying the resolution of the velocity streamlines. Default is 1.
streamline_n: An optional numeric value specifying the number of velocity streamlines to draw. Default is 15.
streamline_width: A numeric vector of length 2 specifying the width of the velocity streamlines. Default is c(0, 0.8).
streamline_alpha: A numeric value specifying the transparency of the velocity streamlines. Default is 1 (fully opaque).
streamline_color: A character string specifying the color of the velocity streamlines.
streamline_palette: A character string specifying the color palette to use for the velocity streamlines. Default is "RdYlBu".
streamline_palcolor: An optional character vector specifying the colors to use for the velocity streamlines. If NULL, the colors will be generated from the streamline_palette.
streamline_bg_color: A character string specifying the background color of the velocity streamlines. Default is "white".
streamline_bg_stroke: A numeric value specifying the background stroke width of the velocity streamlines. Default is 0.5.
aspect.ratio: A numeric value specifying the aspect ratio of the plot.
title: A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
subtitle: A character string specifying the subtitle of the plot.
xlab: A character string specifying the x-axis label.
ylab: A character string specifying the y-axis label.
legend.position: A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".
legend.direction: A character string specifying the direction of the legend.
theme: A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".
theme_args: A list of arguments to pass to the theme function.
return_layer: A logical value indicating whether to return the ggplot layer instead of the full plot. Default is FALSE.
seed: The random seed to use. Default is 8525.

Value

A ggplot object representing the cell velocity plot or a ggplot layer if return_layer is TRUE.

Examples

# \donttest{
data(dim_example)
VelocityPlot(dim_example[, 1:2], dim_example[, 3:4])

VelocityPlot(dim_example[, 1:2], dim_example[, 3:4], group_by = dim_example$clusters)

VelocityPlot(dim_example[, 1:2], dim_example[, 3:4], plot_type = "grid")

VelocityPlot(dim_example[, 1:2], dim_example[, 3:4], plot_type = "stream")

# }

Usage

Arguments

Value

See also

Examples