Velocity Plot

This function creates a velocity plot for a given Seurat object. The plot shows the velocity vectors of the cells in a specified reduction space.

Usage

VelocityPlot(
  srt,
  reduction,
  dims = c(1, 2),
  cells = NULL,
  velocity = "stochastic",
  plot_type = c("raw", "grid", "stream"),
  group.by = NULL,
  group_palette = "Paired",
  group_palcolor = NULL,
  n_neighbors = ceiling(ncol(srt@assays[[1]])/50),
  density = 1,
  smooth = 0.5,
  scale = 1,
  min_mass = 1,
  cutoff_perc = 5,
  arrow_angle = 20,
  arrow_color = "black",
  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_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE,
  seed = 11
)

Arguments

srt: A Seurat object.
reduction: Which dimensionality reduction to use. If not specified, will use the reduction returned by DefaultReduction.
dims: Dimensions to plot, must be a two-length numeric vector specifying x- and y-dimensions
cells: A character vector of cell names to use.
velocity: Name of the velocity to use for plotting. Default is "stochastic".
plot_type: Type of plot to create. Can be "raw", "grid", or "stream".
group.by: Name of one or more meta.data columns to group (color) cells by.
group_palette: Name of the palette to use for coloring the groups. Defaults is "Paired".
group_palcolor: Colors to use for coloring the groups. Defaults is NULL.
n_neighbors: Number of neighbors to include for the density estimation. Defaults is ceiling(ncol(srt@assays[[1]]) / 50).
density: Proportion of cells to plot. Defaults is 1 (plot all cells).
smooth: Smoothing parameter for density estimation. Defaults is 0.5.
scale: Scaling factor for the velocity vectors. Defaults is 1.
min_mass: Minimum mass value for the density-based cutoff. Defaults is 1.
cutoff_perc: Percentile value for the density-based cutoff. Defaults is 5.
arrow_angle: Angle of the arrowheads. Defaults is 20.
arrow_color: Color of the arrowheads. Defaults is "black".
streamline_L: Length of the streamlines. Defaults is 5.
streamline_minL: Minimum length of the streamlines. Defaults is 1.
streamline_res: Resolution of the streamlines. Defaults is 1.
streamline_n: Number of streamlines to plot. Defaults is 15.
streamline_width: Width of the streamlines. Defaults is c(0, 0.8).
streamline_alpha: Alpha transparency of the streamlines. Defaults is 1.
streamline_color: Color of the streamlines. Defaults is NULL.
streamline_palette: Name of the palette to use for coloring the streamlines. Defaults is "RdYlBu".
streamline_palcolor: Colors to use for coloring the streamlines. Defaults is NULL.
streamline_bg_color: Background color of the streamlines. Defaults is "white".
streamline_bg_stroke: Stroke width of the streamlines background. Defaults is 0.5.
aspect.ratio: Aspect ratio of the panel. Default is 1.
title: The text for the title. Defaults is "Cell velocity".
subtitle: The text for the subtitle for the plot which will be displayed below the title. Default is NULL.
xlab: The x-axis label of the plot. Default is NULL.
ylab: The y-axis label of the plot. Default is NULL.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
return_layer: Whether to return the plot layers as a list. Defaults is FALSE.
seed: Random seed for reproducibility. Default is 11.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- standard_scop(pancreas_sub)
pancreas_sub <- RunSCVELO(
  pancreas_sub,
  group.by = "SubCellType",
  linear_reduction = "pca",
  nonlinear_reduction = "umap",
  return_seurat = TRUE
)
VelocityPlot(
  pancreas_sub,
  reduction = "UMAP"
)

VelocityPlot(
  pancreas_sub,
  reduction = "UMAP",
  group.by = "SubCellType"
)

VelocityPlot(
  pancreas_sub,
  reduction = "UMAP",
  plot_type = "grid"
)

VelocityPlot(
  pancreas_sub,
  reduction = "UMAP",
  plot_type = "stream"
)

VelocityPlot(
  pancreas_sub,
  reduction = "UMAP",
  plot_type = "stream",
  streamline_color = "black"
)

VelocityPlot(
  pancreas_sub,
  reduction = "UMAP",
  plot_type = "stream",
  streamline_color = "black",
  arrow_color = "red"
)
} # }

Usage

Arguments

See also

Examples