Joint t-SNE visualization of the velocities by joint t-SNE embedding of both current and extraploated cell positions
tSNE.velocity.plot(vel, cell.colors = NULL, scale = "log",
do.par = T, delta.norm = TRUE, nPcs = 15, norm.nPcs = nPcs * 10,
perplexity = ncol(vel$current)/3, show.grid.flow = FALSE,
grid.n = 20, grid.sd = NULL, min.grid.cell.mass = 1,
pcount = 0.1, verbose = TRUE, min.arrow.median.ratio = 1/10,
max.arrow.quantile = 0.9, arrow.scale = 1, arrow.lwd = 1,
xlab = "", ylab = "", n.cores = defaultNCores(),
size.norm = TRUE, ...)velocity result
named color vector for the cells
whether to rescale current/projected
whether to reset par (default=T)
whether to renormalize velocities following PCA projection
number of PCs onto which project the velocities
number of PCs to use for velocity normalization
perplexity parameter to use in joint t-SNE calculation
whether grid flow pattern should be drawn
number of grid points along each axis
standard deviation of each grid point (used to determine the averaging radius for each grid point)
minimal number of cells around a grid point required for the grid point to show up
pseudocount
whether to show messages
minimal ratio of arrow length (to the median arrow length) below which the arrows are not drawn (default=1/10)
max arrow quantile that's used for arrow size calculation (default=0.9)
scaling factor for the arrows
arrow line width
x axis label
y axis label
number of cores to use
whether to re-normalize current and projected cell sizes
extra parameters are passed to plot() routine.
invisible list containing embedding positions of current state (current.emb) and extrapolated states (projected.emb)