tSNE.velocity.plot: Joint t-SNE visualization of the velocities by joint t-SNE...

Description Usage Arguments Value

View source: R/momentum_routines.R

Description

Joint t-SNE visualization of the velocities by joint t-SNE embedding of both current and extraploated cell positions

Usage

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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,
  ...
)

Arguments

vel

velocity result

cell.colors

named color vector for the cells

scale

whether to rescale current/projected

do.par

whether to reset par (default=T)

delta.norm

whether to renormalize velocities following PCA projection

nPcs

number of PCs onto which project the velocities

norm.nPcs

number of PCs to use for velocity normalization

perplexity

perplexity parameter to use in joint t-SNE calculation

show.grid.flow

whether grid flow pattern should be drawn

grid.n

number of grid points along each axis

grid.sd

standard deviation of each grid point (used to determine the averaging radius for each grid point)

min.grid.cell.mass

minimal number of cells around a grid point required for the grid point to show up

pcount

pseudocount

verbose

whether to show messages

min.arrow.median.ratio

minimal ratio of arrow length (to the median arrow length) below which the arrows are not drawn (default=1/10)

max.arrow.quantile

max arrow quantile that's used for arrow size calculation (default=0.9)

arrow.scale

scaling factor for the arrows

arrow.lwd

arrow line width

xlab

x axis label

ylab

y axis label

n.cores

number of cores to use

size.norm

whether to re-normalize current and projected cell sizes

...

extra parameters are passed to plot() routine.

Value

invisible list containing embedding positions of current state (current.emb) and extrapolated states (projected.emb)


sqjin/nlvelo documentation built on Feb. 11, 2021, 8:09 a.m.