glines-methods {flowViz} | R Documentation

## 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.

### Details

When plotting code{flowFrame}s 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`s assuming that they are defined for the repective 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 code{base} `lines` 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` 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`s.
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`s.
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`s.
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

### Author(s)

F. Hahne

### See Also

`filter`, `flowFrame`, `glines`, `gpoints`

[Package flowViz version 1.6.2 Index]