Description Usage Arguments Value
View source: R/momentum_routines.R
based on Euclidean distance of the extrapolated cell to others The direction of the arrow is towards n closest neighbors. The magnitude of the arrow is determined by the cosine projection of the velocity on to the chosen direction n=1 will only show arrows for cells that end up being projected closer to some other cell than to the original position n=k (k>1) will show an average direction Given an expression distance between cells d, and ratio of extrapolated to current expression distances between cells f, the transition probability is calculated as exp(- (d*(f^beta))^2/(2*sigma^2) )
1 2 3 4 5 6 7 8 9 10 | show.velocity.on.embedding.eu(emb, vel, n = 30, embedding.knn = TRUE,
cell.colors = NULL, sigma = NA, beta = 1, arrow.scale = 1,
scale = "log", nPcs = NA, arrow.lwd = 1, xlab = "", ylab = "",
control.for.neighborhood.density = TRUE, ntop.trajectories = 1,
do.par = T, show.cell.arrows = NULL, show.cell.trajectories = NULL,
show.trajectories = FALSE, show.all.trajectories = FALSE,
show.cell.diffusion.posterior = NULL, show.grid.flow = FALSE,
diffusion.steps = 10, cell.dist = NULL,
trajectory.spline.shape = 1, cell.color.alpha = 0.5,
n.cores = defaultNCores(), n.trajectory.clusters = 10, ...)
|
emb |
embedding to be used for projection |
vel |
velocity result |
n |
neighborhood size (default=30) |
embedding.knn |
pre-calculated kNN |
cell.colors |
named color vector for cell plotting |
sigma |
sigma to use in calculating transition probability from the eucledian distance (estimated automatically by default) |
beta |
beta parameter used in calculation of transition probability (by default=1) |
arrow.scale |
additional scaling factor for the arrows (default=1) |
scale |
scale to use in calculating distances (default: 'log', also supported 'sqrt' |
nPcs |
number of PCs to project the cells onto (to perform distance calculations in lower dimensions), default=NA which turns off PCA dimensional reduction |
arrow.lwd |
arrow line width |
xlab |
x axis label |
ylab |
y axis label |
control.for.neighborhood.density |
compensate for cell density variations in the embedding (default: TRUE) |
ntop.trajectories |
number of top trajectories to trace back for a given cell (when show.trajectories=TRUE) |
do.par |
whether to reset plotting parameters (default=TRUE) |
show.cell.arrows |
show detailed velocity projection for the specified cell |
show.cell.trajectories |
show trajectories for a specified cell |
show.trajectories |
show top median diffusion trajectories |
show.all.trajectories |
show all diffusion paths (messy) |
show.cell.diffusion.posterior |
show diffusion posterior of a given cell |
show.grid.flow |
show velocity projections on a grid |
diffusion.steps |
number of diffusion steps to take forward (default=10) |
cell.dist |
- optional custom distance (must include all of the cells that are intersecting between emb and vel) |
trajectory.spline.shape |
shape parameter for smoothing median cell trajectories (default=1) |
cell.color.alpha |
trasparency parameter to apply when showing cell colors |
n.cores |
number of cores to use in calculations |
n.trajectory.clusters |
number of trajectory clusters to show median paths for (when show.trajectories=TRUE) |
... |
extra parameters are passed to the plot() function |
transition probability matrix
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