Skip to contents

Cell Velocity Plot

Source: R/celldimplot.R
CellVelocityPlot.Rd

This function creates a cell velocity plot for a Seurat object, a Giotto object, a path to an .h5ad file or an opened H5File by hdf5r package. It allows for various customizations such as grouping by metadata, adding edges between cell neighbors, highlighting specific cells, and more. This function is a wrapper around plotthis::VelocityPlot(), which provides a flexible way to visualize cell velocities in reduced dimensions. This function extracts the cell embeddings and velocity embeddings from the Seurat or Giotto object and passes them to plotthis::VelocityPlot().

Usage

CellVelocityPlot(
  object,
  reduction,
  v_reduction,
  spat_unit = NULL,
  feat_type = NULL,
  group_by = NULL,
  ...
)

Arguments

object

A seurat object, a giotto object, a path to an .h5ad file or an opened H5File by hdf5r package.

reduction

Name of the reduction to plot (for example, "umap").

v_reduction

Name of the velocity reduction to plot (for example, "stochastic_umap"). It should be the same as the reduction used to calculate the velocity.

spat_unit

The spatial unit to use for the plot. Only applied to Giotto objects.

feat_type

feature type of the features (e.g. "rna", "dna", "protein"), only applied to Giotto objects.

group_by

A character vector of metadata column name(s) to group (color) the data. Default is NULL.

...

Other arguments passed to plotthis::VelocityPlot().

Value

A ggplot object

Details

See:

for examples of using this function with .h5ad files.

See also

CellDimPlot()

Examples

# \donttest{
data(pancreas_sub)

CellVelocityPlot(pancreas_sub, reduction = "PCA", v_reduction = "stochastic_PCA")

CellVelocityPlot(pancreas_sub, reduction = "PCA", v_reduction = "stochastic_PCA",
 plot_type = "grid")

CellVelocityPlot(pancreas_sub, reduction = "PCA", v_reduction = "stochastic_PCA",
 plot_type = "stream")

CellVelocityPlot(pancreas_sub, reduction = "PCA", v_reduction = "stochastic_PCA",
 group_by = "SubCellType")

# }