NEWS.md

In RGLab/CytoML: A GatingML Interface for Cross Platform Cytometry Data Sharing

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_gatingsetto 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

RGLab/CytoML documentation built on Feb. 1, 2024, 12:34 a.m.