ContinuousEVF: Generating EVFs for cells sampled along the trajectory of...

In YosefLab/SymSim: Simulate Single Cell RNA Sequencing Data

Generating EVFs for cells sampled along the trajectory of cell development

Description

Generating EVFs for cells sampled along the trajectory of cell development

Usage

ContinuousEVF(
  phyla,
  ncells,
  n_nd_evf,
  n_de_evf,
  impulse = F,
  evf_center = 1,
  vary = "s",
  Sigma,
  plotting = T,
  plotname = "cont_evf.pdf",
  seed
)

Arguments

phyla	tree for cell developement
ncells	number of cells
n_nd_evf	Number of EVFs that do not have an impulse signal
n_de_evf	Number of EVFs with an impulse signal
impulse	if the impluse model should be used instead of Brownian motion
evf_center	the mean of Gaussain function where the non-Diff EVFs are sampled from
vary	which parameters are affected by Diff-EVFs. Can be "kon", "koff", "s", "all", "except_kon", "except_koff", "except_s". Suggestions are "all" or "s"
Sigma	The standard deviation of the brownian motion of EVFs changing along the tree
plotting	Whether to plot the trajectory or not
plotname	The string to be used in the output file name
seed	the random seed
tip	The leaf that the path with impulse lead to

Value

a list of two object, one is the evf, and the other is a dataframe indicating the branch each cell comes from (pop) and its depth in the tree (depth)

YosefLab/SymSim documentation built on Sept. 30, 2024, 2:22 p.m.