Velocity stream plot in low-dimensional space

Plot velocities embedded into low-dimensional space as a stream plot. Stream lines are lines that follow the gradient in the velocity field and illustrate paths that cells could follow based on observed RNA velocities.

Usage

plotVelocityStream(
  sce,
  embedded,
  use.dimred = 1,
  color_by = "#444444",
  color.alpha = 0.2,
  grid.resolution = 60,
  scale = TRUE,
  stream.L = 10,
  stream.min.L = 0,
  stream.res = 4,
  stream.width = 8,
  color.streamlines = FALSE,
  color.streamlines.map = c("#440154", "#482576", "#414487", "#35608D", "#2A788E",
    "#21908C", "#22A884", "#43BF71", "#7AD151", "#BBDF27", "#FDE725"),
  arrow.angle = 8,
  arrow.length = 0.8
)

Arguments

sce: A SingleCellExperiment object containing low-dimensional coordinates, e.g., after t-SNE, in its reducedDims.
embedded: A low-dimensional projection of the velocity vectors into the embedding of sce. This should be of the same dimensions as sce and is typically produced by embedVelocity.
use.dimred: String or integer scalar specifying the reduced dimensions to retrieve from sce.
color_by: A character scalar specifying a column in colData(sce) to color cells in the phase graph. Alternatively, color_by can be set to a valid R color to be used to color cells.
color.alpha: An integer scalar giving the transparency of colored cells. Possible values are between 0 (fully transparent) and 1.0 (opaque).
grid.resolution: Integer scalar specifying the resolution of the grid, in terms of the number of grid intervals along each axis.
scale: Logical scalar indicating whether the averaged vectors should be scaled by the grid resolution.
stream.L: Integer scalar giving the typical length of a streamline low-dimensional space units.
stream.min.L: A numeric scalar with the minimum length of segments to be shown.
stream.res: Numeric scalar specifying the resolution of estimated streamlines (higher numbers increase smoothness of lines but also the time for computation).
stream.width: A numeric scalar controlling the width of streamlines.
color.streamlines: Logical scalar. If TRUE streamlines will be colored by local velocity. Arrows cannot be shown in that case.
color.streamlines.map: A character vector specifying the color range used for mapping local velocities to streamline colors. The default is viridisLite::viridis(11).
arrow.angle, arrow.length: Numeric scalars giving the angle and length of arrowheads.

Value

A ggplot2 object with the streamline plot.

Details

grid.resolution and scale are passed to gridVectors, which is used to summarized the velocity vectors into an initial grid. A full regular grid is computed from that and used in geom_streamline to calculate streamlines. The following arguments are passed to the arguments given in parenthesis of geom_streamline: stream.L (L), stream.res (res), stream.min.L (min.L), arrow.angle (arrow.angle) and arrow.length (arrow.length). Streamlines are computed by simple integration with a forward Euler method, and stream.L and stream.res are used to compute the number of steps and the time interval between steps for the integration. stream.width is multiplied with ..step.. estimated by geom_streamline to control the width of streamlines.

Author

Michael Stadler

Examples

library(scuttle)
set.seed(42)
sce1 <- mockSCE(ncells = 100, ngenes = 500)
sce2 <- mockSCE(ncells = 100, ngenes = 500)

datlist <- list(X=counts(sce1), spliced=counts(sce1), unspliced=counts(sce2))

out <- scvelo(datlist, mode = "dynamical")

em <- embedVelocity(reducedDim(out, 1), out)[,1:2]
#> ℹ Using the 'X' assay as the X matrix

# https://github.com/kevinrue/velociraptor/issues/90

if (!basilisk.utils::isMacOSX()){
plotVelocityStream(out, em)
plotVelocityStream(out, em, color.streamlines = TRUE)
}
#> Warning: The dot-dot notation (`..step..`) was deprecated in ggplot2 3.4.0.
#> ℹ Please use `after_stat(step)` instead.
#> ℹ The deprecated feature was likely used in the velociraptor package.
#>   Please report the issue at <https://github.com/kevinrue/velociraptor/issues>.