plot-methods {flowFP} | R Documentation

## Methods for visualizing flowFP objects

### Description

These methods allow the user to plot flowFP objects with a number of options.

### Methods

`plot (x, y, ...)`

`x = "flowFPModel", y = "missing"`

  Visualize a `flowFPModel`.
  Optional Args: `(parameters=NULL, alpha=1, border="gray", showbins=1:nFeatures(x), ylim=NULL, xlim=NULL, main="Model", ...)`

`x = "flowFPModel", y = "flowFrame"`

  Visualize a `flowFPModel` along with a `flowFrame`.
  Optional Args: `(parameters=NULL, alpha=1, border="gray", showbins=1:nFeatures(x), ylim=NULL, xlim=NULL, main="Model", ...)`

`x = "flowFPModel", y = "flowSet"`

  Visualize a `flowFPModel` along with a `flowSet`.
  Optional Args: `(parameters=NULL, alpha=1, border="gray", showbins=1:nFeatures(x), ylim=NULL, xlim=NULL, main="Model", ...)`

`x = "flowFP", y = "missing"`

  Visualize Fingerprints.
  Optional Args: `(type=c("tangle", "stack", "grid", "qc", "plate"), ...)`
  See Notes for additional details.

`x = "flowFP", y = "flowFrame"`

  Visualize a single fingerprint with a flowFrame. See Notes.

`x = "flowFP", y = "flowSet"`

  Visualize Fingerprints with a flowSet.
  Optional Args: `(x, y, showbins=NULL, showfp=TRUE, ...)`

`x = "flowFPPlex", y = "missing"`

  Visualize Fingerprints in a flowFPPlex.
  Optional Args: `(type=c("tangle", "stack", "grid","qc", "plate"), ...)`

### Arguments

`parameters`

  Flow parameters involved in fingerprinting.

`showbins`

  Which bins to render. May be an integer, list of integers, or boolean. Default: 1:nFeatures(x).

`showfp`

  Boolean. Do we want to see the fingerprints (TRUE) or just the parameter plot (FALSE).

`xlim`

  Range of values for the x-axis. Default: range of the data.

`ylim`

  Range of values for the y-axis. Default: range of the data.

`type`

  Specify the type of plot. Current values supported are: “tangle”, “stack”, “grid”, “qc”, “plate”.

`transformation`

  Specify transformation. Values may be: “raw”, “normalized”, “log2norm”

`useClasses`

  Boolean. Colors lines by sampleClass. Default=FALSE.

`linecols`

  Specify color(s) for fingerprint lines. Default = ‘black’. When used in conjunction with `useClasses`, this can be a list of colors whose length matches the number of levels in the `sampleClasses` factor object.

`alpha`

  Opacity of rectangles representing bins.

`border`

  Color to draw the border of a bin. Default: ‘gray’.

`highlight`

  Which fingerprints to highlight. Default=`1:length(x)`.

`main`

  Title for the plot. Default: various.

`xlab`

  Label for the x-axis.

`vert_scale`

  Sets the vertical scale for some plots.

`respect`

  Boolean. If TRUE, respect a square aspect ratio.

`method`

  Determine QC metric for fingerprint deviation. Either `sd` (standard deviation) or `max` (maximum deviation).

`red_limit`

  Value corresponding to a red color for the QC metric.

`...`

  Other parameters passed through to generic `plot`.

### Notes

In conjunction with showbins:

  generic plot args such as `pch` and `cex` can be used to visualize events in specific bins.

For type=“tangle” methods:

  Optional Args: `(transformation=c("raw", "normalized", "log2norm"), linecols=NULL, highlight=NULL, ylim=NULL, useClasses=FALSE, main="Fingerprints", xlab='Feature Index', ...)`

For type=“stack” methods:

  Optional Args: `(transformation=c("raw", "normalized", "log2norm"), linecols=NULL, useClasses=FALSE, vert_scale=3, ylim=NULL, main="Fingerprints",...)`

For type=“grid” methods:

  Optional Args: `(vert_scale=3, main="Fingerprints", linecols="black", transformation=c("raw", "normalized", "log2norm"), respect=FALSE)`

For type=“qc” methods:

  Optional Args: `(main="Fingerprint Deviation Plot", transformation=c("log2norm", "raw", "normalized"), vert_scale=3, method=c("sd", "max"), red_limit=1.0, respect=FALSE)`

For type=“plate” methods:

  Optional Args: `(main="Fingerprint Deviation Plot", transformation=c("log2norm", "raw", "normalized"), vert_scale=3, method=c("sd", "max"), red_limit=1.0)`

[Package flowFP version 1.40.1 Index]