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CytoML 1.0.0

  • First submission

CytoML 1.1.2

  • support diva workspace parsing

CytoML 1.11.11 (Bioconductor 3.10)

API Changes

  • Change handling of quad gates according to RGLab/cytolib#16

  • Renaming of methods:

    • openWorkspace -> open_diva_xml, open_flowjo_xml
    • cytobankExperiment -> open_cytobank_experiment
    • cytobank2GatingSet -> cytobank_to_gatingset
    • parseWorkspace -> flowjo_to_gatingset, diva_to_gatingset
    • getSampleGroups -> fj_ws_get_sample_groups, diva_get_sample_groups
    • getSamples -> fj_ws_get_samples, diva_get_samples
    • getKeywords -> fj_ws_get_keywords
    • getCompensationMatrices -> ce_get_compensations
    • getTransformation -> ce_get_transformations
    • compare.counts -> gs_compare_cytobank_counts

  • Renaming of classes:

    • divaWorkspace -> diva_workspace
    • flowJoWorkspace -> flowjo_workspace

  • Add CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespace

Fixes/internal changes

  • Make gatingset_to_cytobank export cytobank ML with attribute namespaces
  • Allow diva_to_gatingset to use compensation matrix from xml
  • Pass ... args from cytobank_to_gatingset appropriately down to FCS parser
  • Fix some issues with scaling of gates parsed from Diva workspace (#64)
  • Guard against unsupported transformations being added to GatingSet during Diva parsing
  • Switch diva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans
  • Fix ported flowUtils::xmlTag to enable self-closing tags
  • Make gating.graphGML lookup tailored gates by FCS name as well as file id
  • Add some flexibility to getSpilloverMat used in gatingset_to_flowjo

CytoML 1.13.x (Bioconductor 3.11)

API Changes

  • Rename argument sampNLoc -> sample_names_from in open_flowjo_xml
  • All parsers (flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet
  • Add trans argument to cytobank_to_gatingset to allow overriding of transformations from gatingML file (#76)
  • gatingset_to_flowjo now uses a docker image with a compiled converter: hub.docker.com/r/wjiang2/gs-to-flowjo
  • Some updates to how flowjo_to_gatingset searches for FCS files (#77)
  • Add include_empty_tree option to flowjo_to_gatingset to include samples without gates
  • Allow gatingset_to_flowjo to take a path to a GatingSet archive directory
  • Add gating_graphGML to replace gating.graphGML method for openCyto::gating generic
  • Filter samples by panel when parsing cytobank experiment and add ce_get_samples, ce_get_panels

Fixes/internal changes

  • Automatic time scaling of samples from FlowJo workspaces now handled by flowjo_to_gatingset RGLab/cytolib#33
  • Handle change to default stringsAsFactors=FALSE in R 4.0
  • Eliminated extra intermediate files left in temp directory during workspace parsing
  • Switch usage of GatingSetList to merge_gs_list
  • Solve some Windows build issues
  • Switch from experimental::filesystem to boost::filesystem in C++ FlowJo parser
  • Add CytoML XSD to installation