workFlow(data, name = "default", env = new.env(parent = emptyenv()))
undo(wf, n=1)environment. The
evaluation environment used for the workFlow. workFlow. workFlow object for the constructorBoth applyParentFilter and undo are called for their
side-effects.workFlow, which
takes a flowFrame or flowSet as only
mandatory input and creates a basic view for that. name:"character". The name of
the workFlow object. tree:"fcTreeReference". A
reference to the graphNEL
objects representing the view structure of the workflow. alias:"fcAliasReference". A
reference to the alias table.journal:"fcJournalReference". A
reference to the journal.env:"environment". The
evaluation environment for the workflow in which all objects will be
stored. signature(wf = "workFlow", action =
"concreteFilter"): Create a new gateActionItem and
gateView from a filter and assign those to
the workflow. signature(wf = "workFlow", action =
"filterList"): Create a new gateActionItem and
gateView from a filterList
and assign those to the workflow. signature(wf = "workFlow", action =
"transformList"): Create a new transformActionItem and
transformView from a transform
and assign those to the workflow. signature(wf = "workFlow", action =
"compensation"): Create a new compensateActionItem and
compensateView from a compensation
and assign those to the workflow.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. signature(x = "missing", value = "ANY", pos =
"workFlow", envir = "missing", inherits = "missing", immediate =
"missing"): see above signature(x = "missing", value = "ANY", pos =
"missing", envir = "workFlow", inherits = "missing", immediate =
"missing"): same as above, but provide custom symbol for the
assignment.signature(x = "character", value = "ANY", pos =
"workFlow", envir = "missing", inherits = "missing", immediate =
"missing"): see abovesignature(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. signature(x = "character", pos = "workFlow", envir
= "missing", mode = "missing", inherits = "missing"): Get an
object identified by symbol x from the environment in the
workFlow. signature(x = "character", pos = "missing", envir =
"workFlow", mode = "missing", inherits = "missing"): see above signature(name = "workFlow", pos = "missing", envir
= "missing", all.names = "missing", pattern = "missing"): List
the content of the environment in the workFlow. signature(name = "workFlow", pos = "missing", envir
= "missing", all.names = "missing", pattern = "character"): see
abovesignature(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. signature(x = "workFlow"): List the identifiers
for all views and
actionItems in the
workFlow. signature(x = "workFlow", y = "missing"): Plot
the structure of the workFlow tree. signature(symbol = "character", envir = "workFlow",
subSymbol = "character"): Remove the object identified by the
symbol symbol from the workFlow. signature(wf = "workFlow", n = "numeric"): Undo
the last n operations on the workFlow. signature(object = "workFlow"): Print details
about the object. signature(object = "workFlow"): Summarize a
view in the workFlow. signature(object = "workFlow"): Return a named vector
of node ids where the names are the human readable names stored in
the alias table. signature(x = "workFlow"): List the names of
the actionItems in the
workFlow. signature(x = "workFlow"): List the names of
only the views in the
workFlow. signature(object = "workFlow"): Return the alias
table for the workFlow.signature(object = "environment"): Return the
alias table from a generic environment. The method tries to find
'fcAliasRef' among the object symbols in the environment. signature(object = "workFlow"): Return the
journal for the workFlow.signature(object = "environment"): Return the
journal from a generic environment. The method tries to find
'fcJournalRef' among the object symbols in the environment. signature(object = "workFlow"): Return the
tree of the workFlow.signature(object = "environment"): Return the
tree from a generic environment. The method tries to find
'fcTreeRef' among the object symbols in the environment. 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).
"view",
"actionItem"