glines-methods: Drawing filter boundaries
In flowViz: Visualization for flow cytometry

Description Usage Arguments Details Author(s) See Also

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.

1 2	## S4 method for signature 'filter,missing' glines(x, data, verbose = TRUE, ...)

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

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.

F. Hahne

filter, flowFrame, gpoints

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