workFlow-class {flowCore} | R Documentation |
Class and methods to organize standard flow cytometry data analysis operation in a concise workflow.
workFlow(data, name = "default", env = new.env(parent = emptyenv())) undo(wf, n=1)
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. |
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
themselve).
A workFlow
object for the constructor
Both applyParentFilter
and undo
are called for their
side-effects.
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.
name
:"character"
. The name of
the workFlow object. tree
:"fcTreeReference"
. A
reference to the graphNEL
objects representing the view structure of the workflow. 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
esentially 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 completetion 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.
Florian Hahne
showClass("view")