Description Usage Arguments Value
View source: R/momentum_routines.R
PCA-based visualization of the velocities
1 2 3 4 5 6 7 8 | pca.velocity.plot(vel, nPcs = 4, cell.colors = NULL, scale = "log",
plot.cols = min(3, nPcs - 1), norm.nPcs = NA, do.par = T,
pc.multipliers = NULL, show.grid.flow = FALSE, grid.n = 20,
grid.sd = NULL, arrow.scale = 1, min.grid.cell.mass = 1,
min.arrow.size = NULL, pcount = 1, arrow.lwd = 1,
size.norm = FALSE, return.details = FALSE,
plot.grid.points = FALSE, fixed.arrow.length = FALSE,
max.grid.arrow.length = NULL, n.cores = defaultNCores(), ...)
|
vel |
velocity estimation (gene-relative or global) |
nPcs |
number of successive PCs to visualize |
cell.colors |
a named vector of cell colors for visualization |
scale |
scale to use for expression state transform (default: 'log', other possible values are 'sqrt','linear') |
plot.cols |
number of columns into which to arrange the plots |
norm.nPcs |
optional total number of PCs to use for velocity magnitude normalization |
do.par |
whether to set up graphical parameters of a plot |
pc.multipliers |
an optional vector multipliers for the cell PC scores (useful for reorienting the PCs) |
show.grid.flow |
whether a grid flow should be shown |
grid.n |
number of grid points (on each axis) |
grid.sd |
standard deviation of the grid |
arrow.scale |
scale multiplier for the velocity estimates |
min.grid.cell.mass |
minimum cellular mass |
min.arrow.size |
minimum size of an arrow to show |
pcount |
pseudocount |
arrow.lwd |
thickness of arrows to plot |
size.norm |
whether to rescale current and projected states by cell size (default=FALSE) |
return.details |
whether to return detailed output |
plot.grid.points |
whether to show dots at every grid point |
fixed.arrow.length |
whether to use fixed-size arrow |
max.grid.arrow.length |
limit to the size of the arrows that could be shown (when fixed.arrow.length=FALSE) |
n.cores |
number of cores to use in the calculations |
... |
extra parameters are passed to plot() function |
If return.details=F, returns invisible list containing PCA info (epc) and projection of velocities onto the PCs (delta.pcs). If return.details=T, returns an extended list that can be passed into p1 app for velocity visualization.
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