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NEWS.md

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dynwrap 1.2.4

  • Resubmission after babelwhale was removed from CRAN.

  • MINOR CHANGE: Added @return documentation to all functions.

dynwrap 1.2.3

  • MINOR CHANGE: Fixes to metadata (documentation, citation entry, broken links).

  • MINOR CHANGE: Use alternative method for checking whether dynmethods is installed.

dynwrap 1.2.2

  • MAJOR CHANGE convert_milestone_percentages_to_progressions(): Rewrite implementation to attain significant speedup.

  • MINOR CHANGE 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 Rscript does not work anymore.

  • MINOR CHANGE add_feature_importance(): Add a function for adding feature importance scores to a trajectory.

  • BUG FIX project_waypoints(): Rename milestone waypoints such that the names are unique.

  • BUG FIX infer_trajectory(): Fix error message printing.

  • BUG FIX: dyndimred is used conditionally.

  • BUG FIX: wrap_expression() and add_expression(): Do not override feature_info when it already exists in dataset.

dynwrap 1.2.1 (2020-05-11)

  • BUG FIX project_trajectory(): Correctly pass parameters.

  • MINOR CHANGES select_waypoints(): Do not recompute waypoints if trajectory already contains some.

  • MINOR CHANGES convert_progressions_to_milestone_percentages(): Solve tapply issues ahead of dplyr 1.0 release.

dynwrap 1.2.0 (2020-03-09)

  • FUNCTIONALITY: Improved RNA velocity handling. Not all features need to be present in the projected expression, allowing integration with standard velocyto.R pipelines.

  • BUG FIX calculate_pseudotime(): Fix pseudotime calculation on branching trajectories (#139).

  • BUG FIX flip_edges(): Also flip dimred_segment_progressions if available.

  • BUG FIX add_root(): Fix rooting for some linear trajectories (#149)

  • MINOR CHANGES: Allow a named vector for groups_id prior information (#154)

  • MINOR CHANGES: Moved orient_topology_to_velocity() to scvelo R package.

  • BUG FIX simplify_trajectory(): handle dimred_milestones and dimred_segments values (#153).

  • BUG FIX add_dimred(): Do not execute example of dyndimred if is not installed.

dynwrap 1.1.4 (11-10-2019)

First CRAN release!

  • BUG FIX: Fixed #142 where the error message was truncated

  • DOCUMENTATION: Added examples to all functions.

dynwrap 1.1.3 (05-06-2019)

  • MINOR CHANGE add_dimred(): Add a separate argument for specifying the projected dimred rather than expecting the projected dimred to be passed as additional columns in dimred.

  • BUG FIX: Fix for dynverse/dyno#52, do specify whether or not to use optional priors when passed.

dynwrap 1.1.2 (08-05-2019)

  • FEATURE: Add leaves_n as prior information

dynwrap 1.1.1 (08-05-2019)

  • BUG FIX: Fixed bug for directed geodesic distances with disconnected gra phs, dynverse/dynplot#37

dynwrap 1.1 (07-05-2019)

  • FEATURE: RNA velocity data can now be included in the wrapper

  • FEATURE: RNA velocity projected expression can now be given to methods

  • FEATURE: Added orient_topology_to_velocity() to orient the edges of a trajectory based on the velocity vectors

  • FEATURE: calculate_geodesic_distances() now has a directed parameter, with which you can calculate directed geodesic distances. Unreachable cells will receive an infinite distance

  • FEATURE: Added projected_trajectory() (ported from dynplot). add_dimred() will now by default also add a projection of the trajectory to the data

dynwrap 1.0.1 (09-04-2019)

  • MINOR CHANGE: infer_trajectory(..., debug = TRUE) will now return commands for both entering the container and running the dyncli::main() function inside the container

  • MINOR CHANGE: Make create_ti_method_definition() actually work

  • DOCUMENTATION: Added examples for each trajectory wrapper

  • DOCUMENTATION: Added vignette discussing wrapper types

  • DOCUMENTATION: Added vignette discussing create_ti_method_definition()

  • BUG FIX: Fixed bug where sink() was not removed after interruption

dynwrap 1.0.0 (28-03-2019)

  • MAJOR CHANGE: Add support for Singularity 3.0, drop support for previous releases of Singularity and singularity-hub.

  • MAJOR CHANGE: dynwrap now always works with sparse count and expression matrices

  • FEATURE: Add create_ti_method_definition() to create a definition from a local script.

  • DOCUMENTATION: Major update of all documentation for dynbenchmark publication

  • MINOR CHANGE: Rename compute_tented_geodesic_distances() to calculate_geodesic_distances()

  • MINOR CHANGE: Harmonisation of function arguments to either dataset or trajectory

dynwrap 0.3.1.2 (01-02-2019)

  • BUG FIX: simplify_replace_edges() would sometimes swap edges in milestone network around, but forget invert percentages.

  • BUG FIX: Close sinks when interupting the R process

  • MINOR CHANGE: Work with new babelwhale, which includes support for singularity 3.0

dynwrap 0.3.1.1 (17-12-2018)

  • CLEAN UP: Removed helper functions that are not required any more: get_env_or_null(), read_rds_or_null() and print_processx().

  • MINOR CHANGE: remove requirement that milestone_ids and cell_ids cannot overlap

dynwrap 0.3.1 (19-11-2018)

  • HOTFIX: Use utils::data() to get access to priors.

dynwrap 0.3.0 (19-11-2018)

  • MINOR CHANGE: Added metadata on the different wrapper types implemented in dynwrap.

  • CLEAN UP: Removed plot_fun argument from create_ti_method().

  • MINOR CHANGE: Replaced mc_cores with more flexible map_fun.

  • MINOR CHANGE: Renamed create_ti_method() to create_ti_method_r(), and create_ti_method_with_container() to create_ti_method_container().

  • CLEAN UP: Drastically reworked create_ti_method_r() and create_ti_method_container(), and the underlying functions for executing a method on a dataset.

  • CLEAN UP: Remove parse_parameter_definition() and thereby dependency on ParamHelpers.

dynwrap 0.2.0 (29-10-2018)

  • BUG FIX: Fixed incorrect calculation of milestone percentage during trajectory simplification. Occurs only in a rare edge case, namely when the order of the milestones in the milestone network is very different from the order of the milestone ids (0475e94).

  • BUG FIX: Fixed suggested dependencies not being installed in the dynwrap containers (#100).

  • FEATURE REMOVAL: Removed feather data format because it's not being used and creates dependency issues every now and again.

  • BUG FIX: devtools:::shim_system.file() has been moved to pkgload:::shim_system.file().

  • TESTING: Solved issue with the unit tests by not using any helpers.

  • MINOR CHANGE: Have docker images build from dynwrap@devel.

  • BUG FIX: Remove option(echo = FALSE) from .Rprofile in recipes because some packages directly rely on standard output from R, so printing the command wreaks havoc.

dynwrap 0.1.0 (07-03-2018)

  • INITIAL RELEASE: dynwrap, functionality for containerised trajectory inference.
  • 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 the trajectory model, such as labelling the milestones and rooting the trajectory