plot_velo: Generate interactive 3D UMAP plot with cones for velocity....

In trichelab/velocessor: The world's dumbest single-cell RNA velocity calculator and loader

Description

The opacity of the cones is manipulated so that dot colors are visible. The provided SingleCellExperiment txis MUST have an element scVelo in its metadata, and that element (a SingleCellExperiment) needs to have a colData column "velocity_pseudotime" unless an argument 'colr' is provided. (Hence the references internally to "COLORING" rather than "COLOR")

Usage

plot_velo(
  txis,
  embed = "UMAP",
  replace = FALSE,
  colr = "velocity_pseudotime",
  flip = FALSE,
  ...
)

Arguments

txis	a SingleCellExperiment with metadata(txis)$scVelo
embed	which reducedDims() element to use for plotting? (UMAP)
replace	replace any existing metadata element embedded? (FALSE)
colr	column(s) to use for colors (default: velocity_pseudotime)
flip	flip the velocity arrows (ghetto CellRank)? (FALSE)
...	optional arguments to pass to plotly::plot_ly()

Value

       a plotly plot

trichelab/velocessor documentation built on Jan. 5, 2022, 6:27 p.m.