Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

add na.rm = T to fix #23 #147

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

add na.rm = T to fix #23 #147

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
30 changes: 15 additions & 15 deletions R/momentum_routines.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1099,7 +1099,7 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
cat("transition probs ... ")
tp <- exp(cc/corr.sigma)*emb.knn
#diag(tp) <- 0; # should we allow the self-corelation for scaling?
tp <- t(t(tp)/Matrix::colSums(tp)); # tp shows transition from a given column cell to different row cells
tp <- t(t(tp)/Matrix::colSums(tp, na.rm = T)); # tp shows transition from a given column cell to different row cells
tp <- as(tp,'dgCMatrix')
cat("done\n")
if(!is.null(show.cell)) {
Expand All @@ -1109,9 +1109,9 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
points(emb,pch=19,col=ac(val2col(tp[rownames(emb),show.cell],gradient.range.quantile=1),alpha=0.5))
points(emb[show.cell,1],emb[show.cell,2],pch=3,cex=1,col=1)
di <- t(t(emb)-emb[i,])
di <- di/sqrt(Matrix::rowSums(di^2))*arrow.scale; di[i,] <- 0;
dir <- Matrix::colSums(di*tp[,i])
dic <- Matrix::colSums(di*(tp[,i]>0)/sum(tp[,i]>0)); # relative to expected kNN center
di <- di/sqrt(Matrix::rowSums(di^2, na.rm = T))*arrow.scale; di[i,] <- 0;
dir <- Matrix::colSums(di*tp[,i], na.rm = T)
dic <- Matrix::colSums(di*(tp[,i]>0)/sum(tp[,i]>0, na.rm = T), na.rm = T); # relative to expected kNN center
dia <- dir-dic;
#browser()
suppressWarnings(arrows(emb[colnames(em)[i],1],emb[colnames(em)[i],2],emb[colnames(em)[i],1]+dic[1],emb[colnames(em)[i],2]+dic[2],length=0.05,lwd=1,col='blue'))
Expand All @@ -1125,12 +1125,12 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
rownames(arsd) <- rownames(emb);

if(expression.scaling) {
tpb <- tp>0; tpb <- t(t(tpb)/colSums(tpb));
tpb <- tp>0; tpb <- t(t(tpb)/colSums(tpb, na.rm = T));
es <- as.matrix(em %*% tp) -as.matrix(em %*% as.matrix(tpb));
# project velocity onto expression shift
#pm <- as.matrix(t(vel$deltaE)/sqrt(colSums(vel$deltaE*vel$deltaE)))[colnames(es),] * (t(es)/sqrt(colSums(es*es)))
#pl <- pmax(0,apply(pm,1,sum))
pl <- pmin(1,pmax(0,apply(as.matrix(vel$deltaE[,colnames(es)]) * es, 2, sum)/sqrt(colSums(es*es))))
pl <- pmin(1,pmax(0,apply(as.matrix(vel$deltaE[,colnames(es)]) * es, 2, sum, na.rm = T)/sqrt(colSums(es*es, na.rm = T))))


arsd <- arsd * pl;
Expand All @@ -1148,8 +1148,8 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.

# set up a grid
cat("grid estimates ... ")
rx <- range(c(range(ars$x0),range(ars$x1)))
ry <- range(c(range(ars$y0),range(ars$y1)))
rx <- range(c(range(ars$x0, na.rm = T),range(ars$x1, na.rm = T)))
ry <- range(c(range(ars$y0, na.rm = T),range(ars$y1, na.rm = T)))
gx <- seq(rx[1],rx[2],length.out=grid.n)
gy <- seq(ry[1],ry[2],length.out=grid.n)

Expand All @@ -1174,8 +1174,8 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
# calculate x and y delta expectations
gw <- Matrix::colSums(cw)
cws <- pmax(1,Matrix::colSums(cw));
gxd <- Matrix::colSums(cw*arsd$xd)/cws
gyd <- Matrix::colSums(cw*arsd$yd)/cws
gxd <- Matrix::colSums(cw*arsd$xd, na.rm = T)/cws
gyd <- Matrix::colSums(cw*arsd$yd, na.rm = T)/cws

al <- sqrt(gxd^2+gyd^2);
vg <- gw>=min.grid.cell.mass & al>=min.arrow.size
Expand Down Expand Up @@ -1205,7 +1205,7 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
scale.int <- switch(scale,'log'=2,'sqrt'=3,1)
#es <- expectedExpressionShift(e=as.matrix(em),tp=tp,scale=scale.int,nthreads=n.cores); colnames(es) <- colnames(em); rownames(es) <- rownames(em);
if(!expression.scaling) { #otherwise it has already been calculated
tpb <- tp>0; tpb <- t(t(tpb)/colSums(tpb));
tpb <- tp>0; tpb <- t(t(tpb)/colSums(tpb, na.rm = T));
#es <- expectedExpressionShift(e=as.matrix(em %*% as.matrix(tpb)),tp=tp,scale=scale.int,nthreads=n.cores); colnames(es) <- colnames(em); rownames(es) <- rownames(em);
es <- as.matrix(em %*% tp) -as.matrix(em %*% as.matrix(tpb));
}
Expand All @@ -1219,8 +1219,8 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
gw <- Matrix::colSums(cw)
cws <- pmax(1,Matrix::colSums(cw));
cw <- t(t(cw)/cws)
gxd <- Matrix::colSums(cw*arsd$xd)
gyd <- Matrix::colSums(cw*arsd$yd)
gxd <- Matrix::colSums(cw*arsd$xd, na.rm = T)
gyd <- Matrix::colSums(cw*arsd$yd, na.rm = T)
al <- sqrt(gxd^2+gyd^2);
vg <- gw>=min.grid.cell.mass & al>=min.arrow.size
if(any(vg)) {
Expand All @@ -1243,8 +1243,8 @@ show.velocity.on.embedding.cor <- function(emb,vel,n=100,cell.colors=NULL, corr.
gw <- Matrix::colSums(cw)
cws <- pmax(1,Matrix::colSums(cw));
cw <- t(t(cw)/cws)
gxd <- Matrix::colSums(cw*arsd$xd)
gyd <- Matrix::colSums(cw*arsd$yd)
gxd <- Matrix::colSums(cw*arsd$xd, na.rm = T)
gyd <- Matrix::colSums(cw*arsd$yd, na.rm = T)
al <- sqrt(gxd^2+gyd^2);
vg <- gw>=min.grid.cell.mass & al>=min.arrow.size
if(any(vg)) {
Expand Down