orderCells: Orders cells according to pseudotime.

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

Description

Learns a "trajectory" describing the biological process the cells are going through, and calculates where each cell falls within that trajectory. Monocle learns trajectories in two steps. The first step is reducing the dimensionality of the data with reduceDimension(). The second is this function. function. This function takes as input a CellDataSet and returns it with two new columns: Pseudotime and State, which together encode where each cell maps to the trajectory. orderCells() optionally takes a "root" state, which you can use to specify the start of the trajectory. If you don't provide a root state, one is selected arbitrarily.

Usage

orderCells(cds, root_state = NULL, num_paths = NULL, reverse = NULL)

Arguments

cds	the CellDataSet upon which to perform this operation
root_state	The state to use as the root of the trajectory. You must already have called orderCells() once to use this argument.
num_paths	the number of end-point cell states to allow in the biological process.
reverse	whether to reverse the beginning and end points of the learned biological process.

Details

The reduction_method argument to reduceDimension() determines which algorithm is used by orderCells() to learn the trajectory. If reduction_method == "ICA", this function uses polygonal reconstruction to learn the underlying trajectory. If reduction_method == "DDRTree", the trajectory is specified by the principal graph learned by the DDRTree() function.

Whichever algorithm you use, the trajectory will be composed of segments. The cells from a segment will share the same value of State. One of these segments will be selected as the root of the trajectory arbitrarily. The most distal cell on that segment will be chosen as the "first" cell in the trajectory, and will have a Pseudotime value of zero. orderCells() will then "walk" along the trajectory, and as it encounters additional cells, it will assign them increasingly large values of Pseudotime.

Value

an updated CellDataSet object, in which phenoData contains values for State and Pseudotime for each cell

monocle documentation built on Nov. 8, 2020, 5:06 p.m.