dynwrap: Representing and Inferring Single-Cell Trajectories
dynwrap contains the code for a common model of single-cell trajectories. The package can:
- Wrap the input data of a trajectory inference method, such as expression and prior information
- Run a trajectory inference method in R, in a docker container or a singularity container
- Wrap the output of a trajectory inference method, such as the pseudotime, a clustering or a branch network, and convert it into a common trajectory model
- Further postprocess and adapt the trajectory model, such as labelling the milestones and rooting the trajectory
Documentation and the API reference for dynwrap can be found at the dyvnerse documentation website: https://dynverse.org/ .
dynwrap was used to wrap 50+ trajectory inference method within docker containers in dynmethods.
The advantage of using a common model is that it allows:
- Comparison between a prediction and a gold standard, eg. using dyneval
- Comparing two predictions
- Easily visualise the trajectory, eg. using dynplot
- Extracting relevant features/genes, eg. using dynfeature
news(package = "dynwrap") or NEWS.md for a full
list of changes.
Recent changes in dynwrap 1.2.2
convert_milestone_percentages_to_progressions(): Rewrite implementation to attain significant speedup.
infer_trajectory(): Infer command (Rscript/python) from file extension if possible and avoid using shebang to execute script, because R CMD check for R 4.0 puts Rscript and R dummy executables on the path before R CMD check. This means
#!/usr/bin/env Rscriptdoes not work anymore.
add_feature_importance(): Add a function for adding feature importance scores to a trajectory.
project_waypoints(): Rename milestone waypoints such that the names are unique.
infer_trajectory(): Fix error message printing.
dyndimredis used conditionally.
add_expression(): Do not override feature_info when it already exists in dataset.
Recent changes in dynwrap 1.2.1 (2020-05-11)
project_trajectory(): Correctly pass parameters.
select_waypoints(): Do not recompute waypoints if trajectory already contains some.
convert_progressions_to_milestone_percentages(): Solve tapply issues ahead of dplyr 1.0 release.