flowViz (version 1.30.1)

glines-methods: Drawing filter boundaries

Description

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

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 or xyplot 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 curv1Filter.

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 outlines 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 rectangleGate directly from the gate definition.

x = "ellipsoidGate", data = "filterResult"

see above

x = "ellipsoidGate", data = "flowFrame"

see above

Details

When plotting flowFrames using the plot or xyplot methods provided by flowViz, the plotted parameters are recorded, which makes it possible to correctly overlay the outlines of filter 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 lines functions.

See Also

filter, flowFrame, gpoints