Phase and velocity graphs for a set of genes

For a each gene in a set of genes, show the phase graph (spliced versus unspliced counts and fitted model) and reduced dimension graphs with cell colored by velocity and (spliced) expression.

Usage

plotVelocity(
  x,
  genes,
  use.dimred = 1,
  assay.splicedM = "Ms",
  assay.unsplicedM = "Mu",
  which.plots = c("phase", "velocity", "expression"),
  genes.per.row = 1,
  color_by = "#222222",
  color.alpha = 0.4,
  colors.velocity = c("#A50026", "#D73027", "#F46D43", "#FDAE61", "#FEE08B", "#FFFFBF",
    "#D9EF8B", "#A6D96A", "#66BD63", "#1A9850", "#006837"),
  colors.expression = c("#440154", "#482576", "#414487", "#35608D", "#2A788E", "#21908C",
    "#22A884", "#43BF71", "#7AD151", "#BBDF27", "#FDE725"),
  max.abs.velo = 0.001
)

Arguments

x: A SingleCellExperiment object with RNA velocity results as returned by scvelo, and low-dimensional coordinates, e.g., after t-SNE, in its reducedDims.
genes: A character vector with one or several genes for which to plot phase and velocity graphs. genes have to be in rownames(x).
use.dimred: String or integer scalar specifying the reduced dimensions to retrieve from x.
assay.splicedM: An integer scalar or string specifying the assay of x containing the moments of spliced abundances.
assay.unsplicedM: An integer scalar or string specifying the assay of x containing the moments unspliced abundances.
which.plots: A character vector specifying which plots to create for each gene. Possible values are "phase", "velocity", "expression" and correspond to the phase graph or reduced dimension graphs with cells colored by velocity or (spliced) expression.
genes.per.row: An integer scalar with the numbers of genes to visualize per row of plots. For example, if which.plots = c("phase","expression") and genes.per.row = 2, the resulting figure will have four plot panels per row.
color_by: A character scalar specifying a column in colData(x) to color cells in the phase graph. Alternatively, color_by can be set to vector of valid R colors, either of length one (recycled for all cells) or of length ncol(x), which will then be used to color cells in the phase graph.
color.alpha: An integer scalar giving the transparency of colored cells. Possible values are between 0 (fully transparent) and 1.0 (opaque).
colors.velocity, colors.expression: Character vectors specifying the color ranges used for mapping velocities and expression values. The defaults are RColorBrewer::brewer.pal(11, "RdYlGn") for the velocities and viridisLite::viridis(11) for the expression values.
max.abs.velo: A numeric scalar greater than zero giving the maximum absolute velocity to limit the color scale for the "velocity" graph.

Value

A patchwork object with the plots selected by which.plot for the genes in genes, arranged in a grid according to genes.per.row.

Details

Please note that plotVelocity will modify parameters of the current graphics device using layout and par, in order to create the layout for the generated graph panels.

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))

out1 <- scvelo(datlist, mode = "steady_state")
out2 <- scvelo(datlist, mode = "dynamical")

plotVelocity(out1, c("Gene_0031","Gene_0268"))

plotVelocity(out2, c("Gene_0031","Gene_0268"))