definition.yml

method:
  id: projected_slingshot
  name: Projected Slingshot
  source: adaptation
  platform: R
  license: Artistic-2.0
  url: https://github.com/kstreet13/slingshot

manuscript:
  doi: 10.1186/s12864-018-4772-0
  google_scholar_cluster_id: '15798146274231272778'
  preprint_date: '2017-04-19'
  publication_date: '2018-06-19'

container:
  docker: dynverse/ti_projected_slingshot
  url: https://github.com/dynverse/ti_projected_slingshot

wrapper:
  type: trajectory
  topology_inference: free
  trajectory_types:
    - linear
    - bifurcation
    - convergence
    - multifurcation
    - binary_tree
    - tree
  input_required: expression
  input_optional:
    - start_id
    - end_id

parameters:
  - id: shrink
    type: numeric
    default: 1
    distribution:
      type: expuniform
      lower: 0
      upper: 1
    description: logical or numeric between 0 and 1, determines whether and how much
      to shrink branching lineages toward their average prior to the split.
  - id: reweight
    type: logical
    default: yes
    description: 'logical, whether to allow cells shared between lineages to be reweighted
      during curve-fitting. If `TRUE`, cells shared between  lineages will be
      weighted by: distance to nearest curve / distance to curve.'
  - id: reassign
    type: logical
    default: yes
    description: logical, whether to reassign cells to lineages at each iteration.
      If TRUE, cells will be added to a lineage when their projection distance to
      the curve is less than the median distance for all cells currently assigned
      to the lineage. Additionally, shared cells will be removed from a lineage if
      their projection distance to the curve is above the 90th percentile and their
      weight along the curve is less than 0.1.
  - id: thresh
    type: numeric
    default: 0.001
    distribution:
      type: expuniform
      upper: 100000
      lower: 1.0e-05
    description: numeric, determines the convergence criterion. Percent change in
      the total distance from cells to their projections along curves must be less
      than thresh. Default is 0.001, similar to principal.curve.
  - id: maxit
    type: integer
    default: 10
    distribution:
      type: uniform
      upper: 50
      lower: 0
    description: numeric, maximum number of iterations, see principal.curve.
  - id: stretch
    type: numeric
    default: 2.0
    distribution:
      type: expuniform
      upper: 5.0
      lower: 0.0e+00
    description: numeric factor by which curves can be extrapolated beyond endpoints.
      Default is 2, see principal.curve.
  - id: smoother
    type: character
    default: smooth.spline
    values:
    - smooth.spline
    - loess
    - periodic.lowess
    description: choice of scatter plot smoother. Same as principal.curve, but "lowess"
      option is replaced with "loess" for additional flexibility.
  - id: shrink.method
    type: character
    default: cosine
    values:
    - cosine
    - tricube
    - density
    description: character denoting how to determine the appropriate amount of shrinkage
      for a branching lineage. Accepted values are the same as for `kernel` in
      `density()` (default is `"cosine"`), as well as `"tricube"` and `"density"`.
      See 'Details' for more.