[BioC] flowCore workflows and logical operations on gate views

[Wong, Chao-Jen]

 Alessandro,

 # Apply GateZ to the UNION of cells in GateD+ and GateC+
 gateZ <- rectangleGate(`FL2-H`=c(1.6,5))
 ##
 ## I am stuck HERE :0)
 ## ?? add(wf,gateZ ,parent=(GateD+ | GateC+)) ??
 ##

 ##############################

You have to apply gateZ to GateD+ and GateC- separately. Every time when you add an action to a workFlow, it create a couple flowSet instances. In plot(wf), each node is a flowSet instance, and you cannot "union" the cells in two different objects.

> gateZ <- rectangleGate(`FL2-H`=c(1.6,5), filterId="gateZonD")
> add(wf,gateZ, parent="GateD+")
> gateZ <- rectangleGate(`FL2-H`=c(1.6,5), filterId="gateZonC")
> add(wf,gateZ, parent="GateC+")
> plot(wf)


 On Fri, 4 Feb 2011 13:41:07 -0800 (PST), "Wong, Chao-Jen" 
 <cwon2 at fhcrc.org> wrote:
> Hi, Alessandro,
>
> What kind of filter you are going to apply to wf[["Lymphocytes+"]] or
> wf[["Monocytes-"]]?  There are four types of actions you can apply to
> a work flow object. They are compensation, transformation (logicle,
> asinh, and etc.), normalization, and gating/filtering (rectangleGate,
> rangeGate, norm2Filter, kmeansFilter and etc.) actions. As long as
> your filtering actions are in these categories, and then of course 
> you
> can apply them to any of the gate views (by specifying the "parent"
> argument). There are some extra gating/filtering actions implemented
> in the flowStats packages that you might find useful.
>
>
> Chao-Jen
>
> ----- Original Message -----
> From: "Alessandro Di Cara" <rmailing at di-cara.com>
> To: bioconductor at r-project.org
> Sent: Thursday, February 3, 2011 2:38:13 PM
> Subject: [BioC] flowCore workflows and logical operations on gate 
> views
>
> Dear List,
>
> I am using the flowCore and flowViz packages to perform some flow
> cytometry analyses on clinical data.
> I find the packages extremely useful.
>
> Some of the gating strategies I have to implement are quite tricky 
> and I
> would like to use the "Work Flows" system
> described in the flowCore reference manual. So far, I find this 
> approach
> very efficient, not only for accessing the intermediate analysis 
> steps
> of my analysis but also for solving memory issues when loading many 
> FCS
> files.
>
> I am stuck with the implementation of logical operations on the gate
> views of a workflow
>
> For example let's say  I have a workflow object "wf" with two gate 
> views
>
> wf[["Lymphocytes+"]]
> wf[["Monocytes-"]]
>
> I would like to apply a filter on cells that are in the
> wf[["Lymphocytes+"]] OR wf[["Monocytes-"]] gate views.
>
> Can this be done using the work flows system?  Would these operations 
> be
> reflected in the work flow graph plot ?
>
> Thank you in advance for you help
>
> All the best,
>
> Alessandro Di Cara
> /
>
> /
>
> 	[[alternative HTML version deleted]]
>
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-- 
Chao-Jen Wong 
Program in Computational Biology 
Division of Public Health Sciences 
Fred Hutchinson Cancer Research Center 
1100 Fairview Avenue N., M1-B514 
PO Box 19024 
Seattle, WA 98109 
206.667.4485 
cwon2 at fhcrc.org