Description Usage Arguments Value
View source: R/momentum_routines.R
Joint t-SNE visualization of the velocities by joint t-SNE embedding of both current and extraploated cell positions
1 2 3 4 5 6 7 8 | 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, ...)
|
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. |
invisible list containing embedding positions of current state (current.emb) and extrapolated states (projected.emb)
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