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