show.velocity.on.embedding.eu: Visualize RNA velocities on an existing embedding using...
In velocyto-team/velocyto.R: RNA velocity estimation in R

based on Euclidean distance of the extrapolated cell to others The direction of the arrow is towards n closest neighbors. The magnitude of the arrow is determined by the cosine projection of the velocity on to the chosen direction n=1 will only show arrows for cells that end up being projected closer to some other cell than to the original position n=k (k>1) will show an average direction Given an expression distance between cells d, and ratio of extrapolated to current expression distances between cells f, the transition probability is calculated as exp(- (d*(f^beta))^2/(2*sigma^2) )

show.velocity.on.embedding.eu(emb, vel, n = 30, embedding.knn = TRUE,
  cell.colors = NULL, sigma = NA, beta = 1, arrow.scale = 1,
  scale = "log", nPcs = NA, arrow.lwd = 1, xlab = "", ylab = "",
  control.for.neighborhood.density = TRUE, ntop.trajectories = 1,
  do.par = T, show.cell.arrows = NULL, show.cell.trajectories = NULL,
  show.trajectories = FALSE, show.all.trajectories = FALSE,
  show.cell.diffusion.posterior = NULL, show.grid.flow = FALSE,
  diffusion.steps = 10, cell.dist = NULL,
  trajectory.spline.shape = 1, cell.color.alpha = 0.5,
  n.cores = defaultNCores(), n.trajectory.clusters = 10, ...)

`emb`	embedding to be used for projection
`vel`	velocity result
`n`	neighborhood size (default=30)
`embedding.knn`	pre-calculated kNN
`cell.colors`	named color vector for cell plotting
`sigma`	sigma to use in calculating transition probability from the eucledian distance (estimated automatically by default)
`beta`	beta parameter used in calculation of transition probability (by default=1)
`arrow.scale`	additional scaling factor for the arrows (default=1)
`scale`	scale to use in calculating distances (default: 'log', also supported 'sqrt'
`nPcs`	number of PCs to project the cells onto (to perform distance calculations in lower dimensions), default=NA which turns off PCA dimensional reduction
`arrow.lwd`	arrow line width
`xlab`	x axis label
`ylab`	y axis label
`control.for.neighborhood.density`	compensate for cell density variations in the embedding (default: TRUE)
`ntop.trajectories`	number of top trajectories to trace back for a given cell (when show.trajectories=TRUE)
`do.par`	whether to reset plotting parameters (default=TRUE)
`show.cell.arrows`	show detailed velocity projection for the specified cell
`show.cell.trajectories`	show trajectories for a specified cell
`show.trajectories`	show top median diffusion trajectories
`show.all.trajectories`	show all diffusion paths (messy)
`show.cell.diffusion.posterior`	show diffusion posterior of a given cell
`show.grid.flow`	show velocity projections on a grid
`diffusion.steps`	number of diffusion steps to take forward (default=10)
`cell.dist`	- optional custom distance (must include all of the cells that are intersecting between emb and vel)
`trajectory.spline.shape`	shape parameter for smoothing median cell trajectories (default=1)
`cell.color.alpha`	trasparency parameter to apply when showing cell colors
`n.cores`	number of cores to use in calculations
`n.trajectory.clusters`	number of trajectory clusters to show median paths for (when show.trajectories=TRUE)
`...`	extra parameters are passed to the plot() function