NEWS.md
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
divaWorkspace -> diva_workspace
flowJoWorkspace -> flowjo_workspace
CytoML.par.set, CytoML.par.get for setting parameters in CytoML namespacegatingset_to_cytobank export cytobank ML with attribute namespacesdiva_to_gatingsetto use compensation matrix from xml... args from cytobank_to_gatingset appropriately down to FCS parserGatingSet during Diva parsingdiva_to_gatingset to using flowjo_log_trans instead of logtGml2_trans
gating.graphGML lookup tailored gates by FCS name as well as file idgetSpilloverMat used in gatingset_to_flowjo
sampNLoc -> sample_names_from in open_flowjo_xml
flowjo/cytobank/diva_to_gatingset) now return GatingSet based on cytoset rather than ncdfFlowSet
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-flowjoflowjo_to_gatingset searches for FCS files (#77)flowjo_to_gatingset to include samples without gatesgatingset_to_flowjo to take a path to a GatingSet archive directorygating_graphGML to replace gating.graphGML method for openCyto::gating generic
ce_get_samples, ce_get_panels
flowjo_to_gatingset RGLab/cytolib#33stringsAsFactors=FALSE in R 4.0GatingSetList to merge_gs_list
experimental::filesystem to boost::filesystem in C++ FlowJo parser