workFlow-class {flowCore}R Documentation

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.

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).

Value

A workFlow object for the constructor

Both 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.

Author(s)

Florian Hahne

See Also

"view", "actionItem"

Examples

showClass("view")

[Package flowCore version 1.46.2 Index]