wishbone: Wishbone pseudotime

In JiekaiLab/SOT: Single-cell Orientation Tracing

Description

Graph based pasudotime infer. Please install python package "wishbone" before using this function.

Usage

wishbone(
  sce,
  usedEmbed,
  start_cell,
  datatype = "scaledata",
  usedDims = NULL,
  condition = NULL,
  usedLevels = NULL,
  plot_genes = NULL,
  branch = TRUE,
  k = 35,
  num_waypoints = 150,
  seed = 1,
  figsize = c(20, 10)
)

Arguments

sce	A SingleCellExperiment object or matrix.
usedEmbed	Specify the reduce dimension type for construct network. See current avaible embedding by reducedDimNames.
start_cell	Character specified a start cell of the trajectory.
datatype	Type of expression used for plot. See current avaible assays by assays.
usedDims	A vector to specify particular dimensions in usedEmbed to calculate.
condition	Used with usedLevels. Specify a condition in colData(sce) for trimming cells.
usedLevels	Used with condition. Only the cells in usedLevels are used for calculating.
plot_genes	A vector of genes id. If plot_genes is not NULL, plot the average smoothing gene expression along the trajectories.
branch	Whether branches exist or not.
k	kNN graph.
num_waypoints	Number of num_waypoints.
seed	Random seed.
figsize	A vector correponding to the figure width and height.

Value

sce object contain pseudotime and branches.

JiekaiLab/SOT documentation built on Jan. 25, 2022, 3:14 p.m.