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
.
generic plot args such as pch
and cex
can be
used to visualize events in specific bins.
Optional Args: (transformation=c("raw", "normalized", "log2norm"),
linecols=NULL, highlight=NULL, ylim=NULL,
useClasses=FALSE, main="Fingerprints", xlab='Feature Index', ...)
Optional Args: (transformation=c("raw", "normalized", "log2norm"),
linecols=NULL, useClasses=FALSE, vert_scale=3,
ylim=NULL, main="Fingerprints",...)
Optional Args: (vert_scale=3, main="Fingerprints", linecols="black",
transformation=c("raw", "normalized", "log2norm"),
respect=FALSE)
Optional Args: (main="Fingerprint Deviation Plot",
transformation=c("log2norm", "raw", "normalized"),
vert_scale=3, method=c("sd", "max"), red_limit=1.0,
respect=FALSE)
Optional Args: (main="Fingerprint Deviation Plot",
transformation=c("log2norm", "raw", "normalized"),
vert_scale=3, method=c("sd", "max"), red_limit=1.0)
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