VelocityPlot: Velocity Plot
In zh542370159/SCP: Single Cell Pipeline

VelocityPlot

R 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.

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.