0.6.0 This version supports importing of flowJo XML workspaces generated using, up to version 9.2 of the Mac OS X version of flowJo. We do not yet support workpsaces generated using the windows version of flowJo. FEATURES: -import flowJo XML workspace from the Mac version. (Greg Finak) -convert GatingHierarchy objects to workflows. (Mike Jiang) -export workflows to flowJo XML workspace readable by Mac version of flowJo (Mose Andre) -netCDF support for large data sets. Based on code contributed by Nisat Gopalakrishnan. KNOWN ISSUES: export to flowJo - flowWorkspace will export the correct compensation matrices, but they will need to apply manually via the menu items in flowJo. - Navigating between graphs of populations is buggy. - export expects to receive a workflow that contains a compensation view and a transformation view as the first two actions in the workflow. import from flowJ - we may not support all gating configurations. The parsing code was written based on examples. If your workspace is not being imported correctly, contact the authors. If your workspace is not being imported correctly because it's generated by flowJo for windows, it is not supported. Are you sure you're trying to import the XML workspace and not the .jo or .wsp file? flowJo 8.2 for MAC. - XML has some differences and there may be issues importing workspaces into R. We have resolved those bugs that we've found but we have not had the opportunity for extensive testing with this version. speed - import can slow for very large workspaces with many gates. CHANGES IN VERSION 3.11.32 Enhancements + stores the axis information in 'axis' slot of 'GatingSet' class to be used by plotGate + allow different orders of colnames of flow data when merging multiple 'GatingSet's into 'GatingSetList' + add hidden nodes support + annotate hidden and boolean nodes in 'gating tree' + wrap 'getNodes' logic into c++ to speed it up + add 'flowJoTrans' function to construct the flowJo-type biexponentioal transformation function + add multiple overlays support to plotGate method + add raw.scale argument to plotGate + add 'subset' S3 function to subset the GatingSet/GatingSetList based on 'pData' + add 'long' format output from 'getPopStats` method + add 'transform' method for 'GatingSet' to transform the flow data associated with the GatingSet and save the transformation functions within 'GatingSet' + add some internal functions ('merge-GatingSet.R') to handle merging 'GatingSets'