VelocityPlot: Velocity Plot

VelocityPlotR Documentation

Velocity Plot

Description

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_scp",
  theme_args = list(),
  return_layer = FALSE,
  seed = 11
)

Arguments

srt

A Seurat object.

reduction

Name of the reduction in the Seurat object to use for plotting.

dims

Indices of the dimensions to use for plotting.

cells

Cells to include in the plot. If NULL, all cells will be included.

velocity

Name of the velocity to use for plotting.

plot_type

Type of plot to create. Can be "raw", "grid", or "stream".

group_by

Name of the column in the Seurat object metadata to group the cells by. Defaults to NULL.

group_palette

Name of the palette to use for coloring the groups. Defaults to "Paired".

group_palcolor

Colors to use for coloring the groups. Defaults to NULL.

n_neighbors

Number of neighbors to include for the density estimation. Defaults to ceiling(ncol(srt@assays[[1]]) / 50).

density

Propotion of cells to plot. Defaults to 1 (plot all cells).

smooth

Smoothing parameter for density estimation. Defaults to 0.5.

scale

Scaling factor for the velocity vectors. Defaults to 1.

min_mass

Minimum mass value for the density-based cutoff. Defaults to 1.

cutoff_perc

Percentile value for the density-based cutoff. Defaults to 5.

arrow_angle

Angle of the arrowheads. Defaults to 20.

arrow_color

Color of the arrowheads. Defaults to "black".

streamline_L

Length of the streamlines. Defaults to 5.

streamline_minL

Minimum length of the streamlines. Defaults to 1.

streamline_res

Resolution of the streamlines. Defaults to 1.

streamline_n

Number of streamlines to plot. Defaults to 15.

streamline_width

Width of the streamlines. Defaults to c(0, 0.8).

streamline_alpha

Alpha transparency of the streamlines. Defaults to 1.

streamline_color

Color of the streamlines. Defaults to NULL.

streamline_palette

Name of the palette to use for coloring the streamlines. Defaults to "RdYlBu".

streamline_palcolor

Colors to use for coloring the streamlines. Defaults to NULL.

streamline_bg_color

Background color of the streamlines. Defaults to "white".

streamline_bg_stroke

Stroke width of the streamlines background. Defaults to 0.5.

aspect.ratio

Aspect ratio of the plot. Defaults to 1.

title

Title of the plot. Defaults to "Cell velocity".

subtitle

Subtitle of the plot. Defaults to NULL.

xlab

x-axis label. Defaults to NULL.

ylab

y-axis label. Defaults to NULL.

legend.position

Position of the legend. Defaults to "right".

legend.direction

Direction of the legend. Defaults to "vertical".

theme_use

Name of the theme to use for plotting. Defaults to "theme_scp".

theme_args

List of theme arguments for customization. Defaults to list().

return_layer

Whether to return the plot layers as a list. Defaults to FALSE.

seed

Random seed for reproducibility. Defaults to 11.

See Also

RunSCVELO CellDimPlot

Examples

data("pancreas_sub")
pancreas_sub <- RunSCVELO(srt = 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")

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.