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.

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.

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.

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 1.50.0 Index]