Skip to content

differences.md

Latest commit

 

History

History
57 lines (47 loc) · 2 KB

differences.md

File metadata and controls

57 lines (47 loc) · 2 KB

Missing functions with respect to R version

  • AlterStructure

    • RemoveNodesbyIDs, CollapseCliques, RewireBranches

  • boot

  • DataVSEdges

  • dim.selection

  • evaluate.structure

  • InferTrimRadius

  • Interactive

  • OverDispersion

  • plotting

    • missing all except PlotPG (for basic functionality)

  • pseudotime

  • computeElasticGraphWithGrammars :

    • missing ParallelRep option

  • GetSubGraph 'branches' does not handle the presence of loops yet

Corrected R version bugs

Several bugs of the R version were corrected. If you downloaded the original R package and notice a difference with this one, please make sure you are using the latest R version

  • typos in function and parameter names:
    • e.g., CollapseBrances -> CollapseBranches, ExtendLeaves('WeigthedCentroid') -> ExtendLeaves('WeightedCentroid')
  • f_reattach_edges :
    • average mistake -> add parentheses
  • Bisectedge :
    • mean function mistake -> concatenate the two arguments
  • ExtendLeaves :
    • assignment Mus = Lambdas -> assignment Mus = Mus
  • CollapseBranches :
    • two successive return statements -> deleted second return statement
    • "if x: false else: false" condition -> if x: true else: false
  • ShiftBranching :
    • BrIds = intersect(BrIds, BrIds) -> BrIds = intersect(BrIds, BrPoints)
  • getPrimitiveGraphStructureBarCode :
    • barcode error : N[names(N)>=3] -> N[as.integer(names(N))>=3]
  • ShrinkEdge :
    • (Connectivities[Edges[i,1]]>=Min_K | Connectivities[Edges[i,1]]>=Min_K)) -> (Connectivities[Edges[i,1]]>=Min_K | Connectivities[Edges[i,2]]>=Min_K))

R version bugs found but not corrected yet

  • PrimitiveElasticGraphEmbdment :

    • prob points option bugged

  • ReportOnPrimitiveGraphEmbdement :

    • nStars wrong (only 3-stars are counted)
    • nRays always 0
    • energy always non penalized

  • AdjustElasticMatrix_initial :

    • does not update AdjustVect in addition to ElasticMatrix ?

  • computeElasticPrincipalGraph:

    • if(is.null(ReduceDimension)){ReduceDimension <- 1:min(dim(Data))} -> 1:ncol(Data) ?