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Metrics to compare two or more trajectories ⚖
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README.md

ℹ️ Tutorials     ℹ️ Reference documentation

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
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

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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