Learn R Programming

flowCore (version 1.38.2)

workFlow-class: Class "workFlow"(deprecated)

Description

Class and methods to organize standard flow cytometry data analysis operation in a concise workflow.

Usage

workFlow(data, name = "default", env = new.env(parent = emptyenv()))
undo(wf, n=1)

Arguments

data
An object of class flowFrame or flowSet for which a basic view is created.
name
A more human-readable name of the view.
env
Object of class environment. The evaluation environment used for the workFlow.
wf
Object of class workFlow.
n
The number of operations to undo.

Value

A workFlow object for the constructorBoth applyParentFilter and undo are called for their side-effects.

Objects from the Class

Objects should be created using the constructor workFlow, which takes a flowFrame or flowSet as only mandatory input and creates a basic view for that.

Slots

name:
Object of class "character". The name of the workFlow object.
tree:
Object of class "fcTreeReference". A reference to the graphNEL objects representing the view structure of the workflow.
alias:
Object of class "fcAliasReference". A reference to the alias table.
journal:
Object of class "fcJournalReference". A reference to the journal.
env:
Object of class "environment". The evaluation environment for the workflow in which all objects will be stored.

Methods

add
signature(wf = "workFlow", action = "concreteFilter"): Create a new gateActionItem and gateView from a filter and assign those to the workflow.
add
signature(wf = "workFlow", action = "filterList"): Create a new gateActionItem and gateView from a filterList and assign those to the workflow.
add
signature(wf = "workFlow", action = "transformList"): Create a new transformActionItem and transformView from a transform and assign those to the workflow.
add
signature(wf = "workFlow", action = "compensation"): Create a new compensateActionItem and compensateView from a compensation and assign those to the workflow.
assign
signature(x = "ANY", value = "ANY", pos = "missing", envir = "workFlow", inherits = "missing", immediate = "missing"): Assign an object to the environment in the workFlow object and return a fcReference to it. The symbol for the object is created as a unique identifier.
assign
signature(x = "missing", value = "ANY", pos = "workFlow", envir = "missing", inherits = "missing", immediate = "missing"): see above
assign
signature(x = "missing", value = "ANY", pos = "missing", envir = "workFlow", inherits = "missing", immediate = "missing"): same as above, but provide custom symbol for the assignment.
assign
signature(x = "character", value = "ANY", pos = "workFlow", envir = "missing", inherits = "missing", immediate = "missing"): see above
assign
signature(x = "fcReference", value = "ANY", pos = "workFlow", envir = "missing", inherits = "missing", immediate = "missing"): same as above, but assign object using an existing fcReference. Note that assigning NULL essentially removes the original object.
[
signature(x = "workFlow", i = "ANY"): Cast a useful error message.
[[
signature(x = "workFlow", i = "ANY"): Treat the workFlow object as a regular environment. Essentially, this is equivalent to get(x, i).
\$
signature(x = "workFlow", name = "character"): Allow for list-like access. Note that completion is only available for views since all other objects in the environment are considered to be internal.
get
signature(x = "character", pos = "workFlow", envir = "missing", mode = "missing", inherits = "missing"): Get an object identified by symbol x from the environment in the workFlow.
get
signature(x = "character", pos = "missing", envir = "workFlow", mode = "missing", inherits = "missing"): see above
ls
signature(name = "workFlow", pos = "missing", envir = "missing", all.names = "missing", pattern = "missing"): List the content of the environment in the workFlow.
ls
signature(name = "workFlow", pos = "missing", envir = "missing", all.names = "missing", pattern = "character"): see above
mget
signature(x = "character", envir = "workFlow", mode = "missing", ifnotfound = "missing", inherits = "missing"): Get multiple objects identified by the symbols in x from the environment in the workFlow.
names
signature(x = "workFlow"): List the identifiers for all views and actionItems in the workFlow.
plot
signature(x = "workFlow", y = "missing"): Plot the structure of the workFlow tree.
Rm
signature(symbol = "character", envir = "workFlow", subSymbol = "character"): Remove the object identified by the symbol symbol from the workFlow.
undo
signature(wf = "workFlow", n = "numeric"): Undo the last n operations on the workFlow.
show
signature(object = "workFlow"): Print details about the object.
summary
signature(object = "workFlow"): Summarize a view in the workFlow.
nodes
signature(object = "workFlow"): Return a named vector of node ids where the names are the human readable names stored in the alias table.
actions
signature(x = "workFlow"): List the names of the actionItems in the workFlow.
views
signature(x = "workFlow"): List the names of only the views in the workFlow.
alias
signature(object = "workFlow"): Return the alias table for the workFlow.
alias
signature(object = "environment"): Return the alias table from a generic environment. The method tries to find 'fcAliasRef' among the object symbols in the environment.
journal
signature(object = "workFlow"): Return the journal for the workFlow.
journal
signature(object = "environment"): Return the journal from a generic environment. The method tries to find 'fcJournalRef' among the object symbols in the environment.
tree
signature(object = "workFlow"): Return the tree of the workFlow.
journal
signature(object = "environment"): Return the tree from a generic environment. The method tries to find 'fcTreeRef' among the object symbols in the environment.

Details

workFlow objects organize standard flow data analysis operations like gating, compensation and transformation in one single object. The user can interact with a workFlow object (e.g. adding operations, removing them, summarizing the results) without having to keep track of intermediate objects and names.

The integral part of a workFlow is an evaluation environment which holds all objects that are created during the analysis. The structure of the whole workflow is a tree, where nodes represent link{view}s (or results of an operation) and edges represent actionItems (or the operations themselves).

See Also

"view", "actionItem"

Examples

Run this code
showClass("view")

Run the code above in your browser using DataLab