[BioC] Adding Multiple quadrantGates of Same Channels to workFlow (flowCore)

Aric Gregson a.gregson at ucla.edu
Tue Nov 15 00:58:09 CET 2011


What I would like to do seems like a common application in analysis and
I am probably missing a very easy way to accomplish this. I would like
to apply a 'memory gate' generated by quadrantGate to both CD4 and CD8
lymphocyte populations. However, there appears to be no way to give
the second gate a unique name for the workFlow. 

I use a quadrantGate to create filters for channels PE.Cy7.A and
PerCP.Cy5.5.A. The quadrantGates are slightly different for the CD4
and CD8 populations (though that does not matter here). The 'action_'
name in the workFlow is different for each one, but the workFlow node
name appears to be the same thus there is no easy way to call the
population for a plot. After adding the gate I must use an arbitrary
gateview ID for plotting, which is not at all convenient especially with

Is there a way around this? Below is a short example.

Thanks, Aric

quadGate.memory.CD4 <- quadrantGate(Data(wf[['CD4+CD8-']]),
                                          alpha=c(0.5, 1),
add(wf, quadGate.memory.CD4, parent="CD4+CD8-")

quadGate.memory.CD8.base <- quadrantGate(Data(wf[['CD4-CD8+']])[[5]],
                                          alpha=c(0.5, 0.9),
add(wf, quadGate.memory.CD8.base, parent="CD4-CD8+")

Warning: 'CD45ra+CCR7+' is not a unique view name in
this workFlow object. You will only be able to access the view using
its UID 'gateViewRef_OkTFWgIFTF'

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