ℹ️ Tutorials ℹ️ Reference
documentation
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.