R: Phase and velocity graphs for a set of genes

plotVelocity {velociraptor}

R Documentation

Phase and velocity graphs for a set of genes

Description

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.

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.

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.

Author(s)

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"))

[Package velociraptor version 1.4.0 Index]