plot-methods: Methods for visualizing flowFP objects
In holyst/flowFP: Fingerprinting for Flow Cytometry

Description Methods Arguments Notes

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

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"), ...)

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.

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)