gpolygon-methods: Drawing filter regions

In flowViz: Visualization for flow cytometry

Description

These methods extend the basic graphics polygon methods for drawing of filter regions. They allow for multiple dispatch, since not all filter types need to be evaluated for plotting, but this decision should be made internally.

Usage

## S4 method for signature 'filter,missing'
gpolygon(x, data, verbose = TRUE, ...)

Arguments

x	filter or filterResult or any derived filter class
data	flowFrame or filterResult or character or missing or ANY
verbose	logical
...	other arguments

Details

When plotting flowFrames using the plot method provided by flowViz, the plotted parameters are recorded, which makes it possible to correctly overlay the outlines of filters assuming that they are defined for the respective parameters. Warnings and error will be cast for the cases where the parameters are non-distinct or ambigious.

The flow parameters plotted can be passed on to any of the methods through the optional channels argument, which always gets precedence over automatically detected parameters.

The methods support all plotting parameters that are available for the base polygon functions.

Methods

x = "filter", data = "missing"

General method for all objects inheriting from filter. This is used as the default when no more explicit method is found. It tries to find the plotted parameters from the internal flowViz.state environment. This only works if the flow data has been plotted using the plot methods provided by this flowViz package.

x = "filterResult", data = "ANY"

General method for all filterResult object. This basically extracts the filter from the filterResult and dispatches on that.

x = "filterResult", data = "flowFrame"

For some filter types we need the raw data to re-evaluate the filter.

x = "curv1Filter", data = "ANY"

We either need a filterResult or the raw data as a flowFrame for curv1Filters.

x = "curv1Filter", data = "flowFrame"

see above

x = "curv1Filter", data = "missing"

see above

x = "curv1Filter", data = "multipleFilterResult"

see above

x = "curv2Filter", data = "ANY"

We either need a filterResult or the raw data as a flowFrame for curv2Filter.

x = "curv2Filter", data = "flowFrame"

see above

x = "curv2Filter", data = "multipleFilterResult"

see above

x = "kmeansFilter", data = "ANY"

We don't know how to plot regions of a kmeansFilter, hence we warn.

x = "norm2Filter", data = "ANY"

We either need a filterResult or the raw data as a flowFrame for norm2Filter.

x = "norm2Filter", data = "flowFrame"

see above

x = "norm2Filter", data = "logicalFilterResult"

see above

x = "polygonGate", data = "character"

We can plot a polygonGate directly from the gate definition.

x = "polygonGate", data = "filterResult"

see above

x = "polygonGate", data = "flowFrame"

see above

x = "quadGate", data = "character"

We can plot a quadGate directly from the gate definition.

x = "quadGate", data = "filterResult"

see above

x = "quadGate", data = "flowFrame"

see above

x = "rectangleGate", data = "character"

We can plot a rectangleGate directly from the gate definition.

x = "rectangleGate", data = "filterResult"

see above

x = "rectangleGate", data = "flowFrame"

see above

x = "ellipsoidGate", data = "character"

We can plot a ellipsoidGate directly from the gate definition.

x = "ellipsoidGate", data = "filterResult"

see above

x = "ellipsoidGate", data = "flowFrame"

see above

Author(s)

F. Hahne

See Also

filter, flowFrame, glines, gpoints

flowViz documentation built on Nov. 8, 2020, 7:53 p.m.