roots (version 1.0)

getTraj: Find a plausible developmental journey

Description

Return a plausible developmental journey

Usage

getTraj(rdmap, tm, sourceCellInds, terminalCellsInd = NULL, momAdj = 0.5,
  w1 = exp(1), w2 = 1, simLen = 50, sim.seed = NULL, varEst = 10)

Arguments

rdmap

reduced dimensionality matrix with cells in rows and dims in columns

tm

Transition matrix

sourceCellInds

Starting sell indices

terminalCellsInd

Terminal cell indices

momAdj

Weighting to adjust momentum. From 0-1. Lower numbers make smaller adjustment to momentum vector.

w1

Parameter - Base used for modifying of tm probs.

w2

Parameter - Multiplifaction factor used for modifying tm probs.

simLen

Maximum number of allowable tranisitons

sim.seed

Random seed for reproducibility

varEst

Number of alternatives to sample for estimating variance.

Value

Returns a data.frame of ordered indices and momentums

Details

Return a plausible developmental journey

Examples

# NOT RUN {
traj <- getTraj(rdmap, tm, startCells, terminalCells)
# }