# 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