pca.velocity.plot: PCA-based visualization of the velocities

In velocyto-team/velocyto.R: RNA velocity estimation in R

Description

PCA-based visualization of the velocities

Usage

pca.velocity.plot(vel, nPcs = 4, cell.colors = NULL, scale = "log",
  plot.cols = min(3, nPcs - 1), norm.nPcs = NA, do.par = T,
  pc.multipliers = NULL, show.grid.flow = FALSE, grid.n = 20,
  grid.sd = NULL, arrow.scale = 1, min.grid.cell.mass = 1,
  min.arrow.size = NULL, pcount = 1, arrow.lwd = 1,
  size.norm = FALSE, return.details = FALSE,
  plot.grid.points = FALSE, fixed.arrow.length = FALSE,
  max.grid.arrow.length = NULL, n.cores = defaultNCores(), ...)

Arguments

vel	velocity estimation (gene-relative or global)
nPcs	number of successive PCs to visualize
cell.colors	a named vector of cell colors for visualization
scale	scale to use for expression state transform (default: 'log', other possible values are 'sqrt','linear')
plot.cols	number of columns into which to arrange the plots
norm.nPcs	optional total number of PCs to use for velocity magnitude normalization
do.par	whether to set up graphical parameters of a plot
pc.multipliers	an optional vector multipliers for the cell PC scores (useful for reorienting the PCs)
show.grid.flow	whether a grid flow should be shown
grid.n	number of grid points (on each axis)
grid.sd	standard deviation of the grid
arrow.scale	scale multiplier for the velocity estimates
min.grid.cell.mass	minimum cellular mass
min.arrow.size	minimum size of an arrow to show
pcount	pseudocount
arrow.lwd	thickness of arrows to plot
size.norm	whether to rescale current and projected states by cell size (default=FALSE)
return.details	whether to return detailed output
plot.grid.points	whether to show dots at every grid point
fixed.arrow.length	whether to use fixed-size arrow
max.grid.arrow.length	limit to the size of the arrows that could be shown (when fixed.arrow.length=FALSE)
n.cores	number of cores to use in the calculations
...	extra parameters are passed to plot() function

Value

If return.details=F, returns invisible list containing PCA info (epc) and projection of velocities onto the PCs (delta.pcs). If return.details=T, returns an extended list that can be passed into p1 app for velocity visualization.

velocyto-team/velocyto.R documentation built on Dec. 8, 2019, 3:07 a.m.