plotppt: Visualize pptree onto embedding

In hms-dbmi/crestree: Analysis of branching branching trajectories from single-cell data

Description

Projects pptree onto embedding (e.g. tSNE)

Usage

plotppt(r, emb, F = NULL, gene = NULL, main = gene, mat = NULL,
  pattern.cell = NULL, pattern.tree = NULL, cex.col = NA,
  tree.col = NULL, cex.main = 0.5, cex.title = 1, cex.tree = 1.5,
  lwd.tree = 1, par = TRUE, tips = FALSE, forks = FALSE,
  subtree = NA, pallete = NULL, ...)

Arguments

r	- pptree object
emb	- (x,y) coordinates data frame (e.g Rtsne $Y result)
F	- coordinates of principal points (optional)
gene	- a gene to show expression of (optional)
mat	- gene vs cell expression matrix (needed if option 'gene' is activated)
pattern.cell	- numeric profile of a quantity for each cell (e.g. expression of a gene or cell cycle stage)
pattern.tree	- numeric profile of a quantity for each principal point (e.g. expression of a gene or cell cycle stage)
cex.col	- color of points
cex.main	- cex of points
cex.title	- cex of title
cex.tree	- cex of principal points
tips	- logical, to draw indecies of tips of the tree. Usefull before usage of cleanup.branches()

hms-dbmi/crestree documentation built on July 11, 2019, 8:04 p.m.