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Metrics to compare two trajectories
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 |
|---|---|---|
| cor<sub>dist</sub> | Geodesic distance correlation | cell positions |
| MSE<sub>rf</sub> | Random Forest MSE | neighbourhood |
| NMSE<sub>rf</sub> | Random Forest Normalised MSE | neighbourhood |
| R<sup>2</sup><sub>rf</sub> | Random Forest R² | neighbourhood |
| NMSE<sub>lm</sub> | Linear regression Normalised MSE | neighbourhood |
| MSE<sub>lm</sub> | Linear regression MSE | neighbourhood |
| R<sup>2</sup><sub>lm</sub> | Linear regression R² | neighbourhood |
| edgeflip | Edge flip | topology |
| HIM | Hamming-Ipsen-Mikhailov similarity | topology |
| Isomorphic | isomorphic | topology |
| F1<sub>branches</sub> | Overlap between the branches | branch assignment |
| F1<sub>milestones</sub> | Overlap between the milestones | branch assignment |
- Application metrics, which assess the accuracy of some downstream analyses of trajectories
| Name | Long name |
|---|---|
| cor<sub>features</sub> | Feature importance correlation |
| wcor<sub>features</sub> | Feature importance weighted correlation |
| ks<sub>feature</sub> | Feature importance enrichment ks |
| wilcox<sub>feature</sub> | 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 |
|---|---|
| mean<sub>harmonic</sub> | Harmonic mean |
| mean<sub>geometric</sub> | Geometric mean |
| mean<sub>arithmetic</sub> | Arithmetic mean |
Latest changes
Check out news(package = "dyneval") or NEWS.md for a
full list of
changes.
Recent changes in dyneval 0.9.9 (07-04-2019)
-
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
Recent changes in dyneval 0.2.2 (21-11-2018)
-
DOCUMENTATION: Update and expand documentation.
-
BUG FIX: Update dyneval for dynwrap 0.3.1 (#50).
-
MINOR CHANGE: Clean up imports and suggests.
Dynverse dependencies
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