flowFP (version 1.30.0)

plot-methods: 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)