This R package implements several metrics for comparing two single-cell trajectories.
These include:
- Specific metrics, metrics which look at the similarity of a specific part of the trajectory, such as the topology or the cellular ordering
| Name | Long name | Category |
|---|---|---|
| cordist | Geodesic distance correlation | cell positions |
| MSErf | Random Forest MSE | neighbourhood |
| NMSErf | Random Forest Normalised MSE | neighbourhood |
| R2rf | Random Forest R² | neighbourhood |
| NMSElm | Linear regression Normalised MSE | neighbourhood |
| MSElm | Linear regression MSE | neighbourhood |
| R2lm | Linear regression R² | neighbourhood |
| edgeflip | Edge flip | topology |
| HIM | Hamming-Ipsen-Mikhailov similarity | topology |
| Isomorphic | isomorphic | topology |
| F1branches | Overlap between the branches | branch assignment |
| F1milestones | Overlap between the milestones | branch assignment |
- Application metrics, which assess the accuracy of some downstream analyses of trajectories
| Name | Long name |
|---|---|
| corfeatures | Feature importance correlation |
| wcorfeatures | Feature importance weighted correlation |
| ksfeature | Feature importance enrichment ks |
| wilcoxfeature | Feature importance enrichment wilcox |
- Overall metrics, which combine several specific and/or application metrics to analyse the overall similarity of two trajectories
| Name | Long name |
|---|---|
| meanharmonic | Harmonic mean |
| meangeometric | Geometric mean |
| meanarithmetic | Arithmetic mean |
Check out news(package = "dyneval") or NEWS.md for a
full list of
changes.
-
MINOR CHANGE: Update categories of metrics
-
MINOR CHANGE: Move metric functions from dyneval to dynutils.
-
MINOR CHANGE: Bump version number for dynwrap 1.0.0
-
DOCUMENTATION: Update and expand documentation.
-
BUG FIX: Update dyneval for dynwrap 0.3.1 (#50).
-
MINOR CHANGE: Clean up imports and suggests.
