show.velocity.on.embedding.cor: Visualize RNA velocities on an existing embedding using...

In sqjin/nlvelo: RNA velocity estimation using nonlinear models

Description

Visualize RNA velocities on an existing embedding using correlation-based transition probability matrix within the kNN graph

Usage

show.velocity.on.embedding.cor(
  emb,
  vel,
  n = 100,
  cell.colors = NULL,
  corr.sigma = 0.05,
  show.grid.flow = FALSE,
  grid.n = 20,
  grid.sd = NULL,
  min.grid.cell.mass = 1,
  min.arrow.size = NULL,
  arrow.scale = 1,
  max.grid.arrow.length = NULL,
  fixed.arrow.length = FALSE,
  plot.grid.points = FALSE,
  scale = "log",
  nPcs = NA,
  arrow.lwd = 1,
  xlab = "",
  ylab = "",
  n.cores = defaultNCores(),
  do.par = T,
  show.cell = NULL,
  cell.border.alpha = 0.3,
  cc = NULL,
  return.details = FALSE,
  expression.scaling = FALSE,
  ...
)

Arguments

emb	embedding onto which to project the velocities; The dimensions of coordinates should be on the order of 10x10 for the default values to make sense.
vel	velocity estimates (e.g. returned by gene.relative.velocity.estimates() )
n	neighborhood size (default=100 cells)
cell.colors	name vector of cell colors
corr.sigma	sigma parameter used to translate velocity-(expression delta) correlation into a transition probability
show.grid.flow	whether to show grid velocity summary
grid.n	number of grid points along each axis
grid.sd	standard deviation (in embedding coordinate space) used to determine the weighting of individual cells around each grid point
min.grid.cell.mass	minimal cell "mass" (weighted number of cells) around each grid point required for it to show up
min.arrow.size	minimal arrow size
arrow.scale	arrow scale multiplier
max.grid.arrow.length	minimal arrow size
fixed.arrow.length	whether to use fixed arrow width (default=FALSE)
plot.grid.points	whether to mark all grid points with dots (even if they don't have valid velocities)
scale	velocity scale to use (default: 'log', other values: 'sqrt','rank','linear')
nPcs	number of PCs to use for velocity regularization (default NA, turns off regularization)
arrow.lwd	arrow width (under fixed.arrow.length=T)
xlab	x axis label
ylab	y axls label
n.cores	number of cores to use
do.par	whether to reset plotting parameters
show.cell	whether to show detailed velocity estimates for a specified cell
cell.border.alpha	transparency for the cell border
cc	velocity-(exprssion delta) correlation matrix (can be passed back from previous results, as $cc) to save calculation time when replotting the same velocity estimates on the same embedding with different parameters
return.details	whether to return detailed output (which can be passed to p1 app for visualization)
expression.scaling	whether to scale the velocity length by the projection of velocity onto the expected expression change (based on the transition probability matrix)
...	extra parameters passed to plot() function

Value

if return.details=F, returns invisible list containing transition probability matrix ($tp) and the velocity-(expression delta) correlation matrix ($cc). If return.details=T, returns a more extended list that can be passed as veloinfo to pagoda2::p2.make.pagoda1.app() for visualization

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