Calculate Correlation of Geodesic Pseudotime Distances — calc_pseudotime

Evaluates whether the relative cell-to-cell ordering along a differentiation trajectory is preserved between reference and simulated data. Accepts either precomputed pseudotime vectors OR scRNA-seq expression matrices (which will be automatically inferred via PCA trajectory).

Usage

calc_pseudotime_correlation(
  ref_pseudotime,
  sim_pseudotime,
  method = c("spearman", "pearson")
)

Arguments

ref_pseudotime: Numeric vector of reference pseudotimes OR reference count matrix (genes x cells).
sim_pseudotime: Numeric vector of simulated pseudotimes OR simulated count matrix (genes x cells).
method: Correlation method: "spearman" (default) or "pearson".

Value

Correlation coefficient between reference and simulated pseudotime trajectories.

Examples

data(example_scrna, package = "scSimEval")
calc_pseudotime_correlation(example_scrna$ref, example_scrna$sim)
#> [1] 1