Full Trajectory Accuracy Evaluation

Evaluates trajectory preservation using pseudotime correlation, branch height discrepancy, and univariate distribution distance metrics on pseudotime. If raw count matrices are provided, pseudotime and lineage trees are automatically inferred directly from the scRNA-seq data.

Usage

evaluate_trajectory_metrics(
  ref_data,
  sim_data,
  cell_types_ref = NULL,
  cell_types_sim = NULL
)

Arguments

ref_data

Reference count matrix (genes x cells) OR numeric vector of pseudotimes.

sim_data

Simulated count matrix (genes x cells) OR numeric vector of pseudotimes.

cell_types_ref

Optional vector of reference cell types (for lineage tree inference).

cell_types_sim

Optional vector of simulated cell types (for lineage tree inference).

Value

A named list of trajectory accuracy metrics.

Examples

data(example_scrna, package = "scSimEval")
evaluate_trajectory_metrics(example_scrna$ref, example_scrna$sim)
#> Metric: 'bhattacharyya' with unit: 'log'; comparing: 2 vectors
#> $pseudotime_correlation
#> [1] 1
#> 
#> $tree_height_rmse
#> [1] NA
#> 
#> $pseudotime_MAD
#> [1] 0.4272106
#> 
#> $pseudotime_KS
#> [1] 0.7973528
#> 
#> $pseudotime_MAE
#> [1] 0.3871033
#> 
#> $pseudotime_RMSE
#> [1] 0.3982072
#> 
#> $pseudotime_OV
#> [1] 0.2252745
#> 
#> $pseudotime_Bhattacharyya
#> [1] 0.006268418
#> 
#> $pseudotime_Wasserstein
#> [1] 0.3871033
#> 
#> $pseudotime_ECDF_DiffArea
#> [1] 0.3877229
#> 
#> $pseudotime_Runs_Statistic
#> [1] -7.772059
#> 
#> $pseudotime_Runs_PValue
#> [1] 3.861015e-15
#> 
#> $pseudotime_NN_Mismatch
#> [1] 0.80625
#> 
#> $pseudotime_Between_Dataset_Silh_Global
#> [1] 0.5144246
#> 
#> $pseudotime_Between_Dataset_Silh_Local
#> [1] 0.6821646
#>