alias,pop,parent,dims,gating_method,gating_args,collapseDataForGating,groupBy,preprocessing_method,preprocessing_args,comments
s,+,root,"FSC-A,FSC-H",singletGate,prediction_level = 0.99,,,,,singlet
v,-,s,Pacific Blue-A,flowClust,"neg = 1, pos = 1",,,prior_flowClust,"neg = 1, pos = 1",remove debris
nonDebris,+,v,FSC-A,mindensity,,TRUE,name,,,get lymph
lymph,+,nonDebris,"FSC-A,SSC-A",flowClust,"K = 2, target = c(100000, 50000)",,,prior_flowClust,,get T cell
cd3,+,lymph,cd3,mindensity,,,,,,get cd4 cut
*,+/-,cd3,cd4,mindensity,,,,,,get cd8- cut
cd8-,-,cd4+,cd8,mindensity,"neg = 1, pos = 1, min = 1000",,,,,get cd8+ cut
cd8+,+,cd4-,cd8,flowClust,"neg = 1, pos = 1, min = 0",,,,,use those cuts to construct quadgate
cd4,+-,cd3,"cd4,cd8",refGate,cd4+:cd8-,,,,,
cd8,-+,cd3,"cd4,cd8",refGate,cd4-:cd8+,,,,,
TNFa,+,cd4,TNFa,tailgate,,,,standardize_flowset,,
IFNg,+,cd4,IFNg,tailgate,,,,standardize_flowset,,
IL2,+,cd4,IL2,tailgate,,,,standardize_flowset,,
TNFa,+,cd8,TNFa,tailgate,,,,standardize_flowset,,
IFNg,+,cd8,IFNg,tailgate,,,,standardize_flowset,,
IL2,+,cd8,IL2,tailgate,,,,standardize_flowset,,
IL2orIFNg,+,cd4,,boolGate,cd4/IL2|cd4/IFNg,,,,,
cd8 subsets,+,cd8,,polyFunctions,cd8/IFNg:cd8/IL2:cd8/TNFa,,,,,
IFNg0.998,+,cd8,IFNg,tailgate,tol = 0.001,,,standardize_flowset,,
