Description Usage Arguments Value
View source: R/momentum_routines.R
Visualize RNA velocities on an existing embedding using correlation-based transition probability matrix within the kNN graph
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | 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,
...
)
|
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 $cc) to save calculation time when replotting the same velocity estimates on the same embedding with different parameters |
return.details |
whether to return detailed output (which can be passed to p1 app for visualization) |
expression.scaling |
whether to scale the velocity length by the projection of velocity onto the expected expression change (based on the transition probability matrix) |
... |
extra parameters passed to plot() function |
if return.details=F, returns invisible list containing transition probability matrix ($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
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