xyplot {flowViz} | R Documentation |
These functions create Trellis scatter plots (a.k.a. dot plots in the Flow Cytometry community) from flow cytometry data.
## methods for 'flowSet' objects ## S4 method for signature 'formula, flowSet': xyplot( x, data, xlab, ylab, as.table=TRUE, prepanel=prepanel.xyplot.flowset, panel=panel.xyplot.flowset, pch = ".", smooth = TRUE, filter = NULL, ...) ## methods for 'flowFrame' objects ## S4 method for signature 'flowFrame, missing': xyplot( x, data, xlab=time, ylab="", time="Time", layout, type="l", smooth=FALSE, ...) ## S4 method for signature 'formula, flowFrame': xyplot( x, data, smooth=TRUE, panel=if(smooth) panel.smoothScatter else panel.xyplot, ...) ## S4 method for signature 'flowFrame, missing': splom( x, data, pscales=0, smooth=TRUE, pch=".", time="Time", exclude.time=TRUE, panel=function(x, y, smooth, ...) { if (smooth) panel.smoothScatter(x, y, ...) else panel.xyplot(x, y, ...) }, ...) ## panel and prepanel functions for flowSets prepanel.xyplot.flowframe.time( x, y, time.x, expr, ...) panel.xyplot.flowframe.time( x, y, time.x, expr, type="l", nrpoints=0, binSize=100, ...) panel.xyplot.flowframe( x, y, frame, filter=NULL, smooth=TRUE, channel.x.name, channel.y.name, pch=".", gpar, ...) ## panel and prepanel functions for flowSets prepanel.xyplot.flowset( x, frames, channel.x, channel.y, ...) panel.xyplot.flowset( x, frames, channel.x, channel.y, channel.x.name, channel.y.name, filter=NULL, pch=".", smooth=TRUE, gpar, ...)
x |
a formula describing the structure of the plot and the
variables to be used in the display. In
prepanel.xyplot.flowset and panel.xyplot.flowset , also
the names of flowFrame s. |
data, y |
a flowSet or
flowFrame object that serves as the source of
data. |
smooth |
logical. If TRUE ,
panel.smoothScatter
is used to display a partially smoothed version of the data.
Otherwise, points are plotted as in a standard scatter plot. |
nrpoints |
|
xlab, ylab |
Labels for data axes, with suitable defaults taken from the formula. |
pch |
the plotting character used when smooth=FALSE . |
type |
type of rendering; see
panel.xyplot for details. For
the basic flowFrame method without a detailed
formula, the addtional type discrete is available, which
plots a smoothed average of the flow cytometry values against
time. |
binSize |
|
prepanel |
the prepanel function. See
xyplot . |
panel |
the panel function. See
xyplot . |
filter |
a filter or
filterResult object or a list of such objects
of the same length as the flowSet to be
superimposed on the plot. The software will figure out whether the
filter needs to be evaluated (in which case
providing a filterResult can speed up things
considerably). |
time |
a character string giving the name of the column recording time. If not provided, we try to guess from the parameter names. |
time.x |
a numeric vector of time values. |
expr |
a numeric matrix of flow cytometry values, basically a
copy of the exprs slot of a flowFrame . |
exclude.time |
logical, specifying whether to exclude the time
variable from a scatter plot matrix. Defaults to TRUE . |
as.table, pscales, layout |
These arguments are passed unchanged to the corresponding methods in lattice, and are listed here only because they provide different defaults. See documentation for the original methods for details. |
channel.x, channel.y |
expressions defining the x and y variables in terms of columns in the data. Can involve functions or multiple columns from the data. |
channel.x.name, channel.y.name |
character strings giving corresponding names, used to match filter parameters if applicable. |
frame, frames |
an environment containing frame-specific data. |
gpar |
an list of graphical parameters that are passed down to
the low level grid functions. See gpar for details. |
... |
more arguments, usually passed on to the underlying lattice methods. |
signature(x = "formula", data = "flowSet")
:
creates scatter plots (a.k.a. dot plots) of a pair of channels signature(x = "flowFrame", data = "missing")
:
produces diagnostic time series plots of all channels against
time. signature(x = "formula", data = "flowFrame")
:
more general scatter plots from a flowFrame
object. The
formula can be fairly general. signature(x = "flowFrame", data = "missing")
:
draws a scatter plot matrix of all channels (excluding time, by
default) of a flowFrame
object.
Not all standard lattice arguments will have the intended effect, but many should. For a fuller description of possible arguments and their effects, consult documentation on lattice.
data(GvHD) ## simple bivariate scatter plot (a.k.a. dot plot) ## by default ('smooth=TRUE') panel.smoothScatter is used xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data = GvHD, layout = c(7, 5)) xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD, layout = c(7, 5)) ## version without smooth xyplot(`SSC-H` ~ `FSC-H` | Visit + Patient, data = GvHD, smooth = FALSE, strip = strip.custom(strip.names = TRUE)) ## several examples with time on the X axis xyplot(`FSC-H` ~ Time | Visit, GvHD, smooth = FALSE, type = "l", subset = (Patient == 5)) xyplot(`FSC-H` ~ Time | Patient:Visit, GvHD, smooth = FALSE, type = "a", strip = FALSE, strip.left = TRUE, aspect = "xy") ## combine plots for two channels ssc.time <- xyplot(`SSC-H` ~ Time | factor(Patient):factor(Visit), GvHD, smooth = FALSE, type = "l", strip = FALSE, strip.left = strip.custom(horizontal = TRUE), par.strip.text = list(lines = 3), between = list(y = rep(c(0, 0.5), c(6, 1))), scales = list(x = list(axs = "i"), y = list(draw = FALSE)), layout = c(1, 35)) fsc.time <- xyplot(`FSC-H` ~ Time | factor(Patient):factor(Visit), GvHD, smooth = FALSE, type = "l", strip = FALSE, strip.left = strip.custom(horizontal = TRUE), par.strip.text = list(lines = 3), between = list(y = rep(c(0, 0.5), c(6, 1))), scales = list(x = list(axs = "i"), y = list(draw = FALSE)), layout = c(1, 35)) plot(fsc.time, split = c(1, 1, 2, 1)) plot(ssc.time, split = c(2, 1, 2, 1), newpage = FALSE) ## saving plots as variables allows more manipulation plot(update(fsc.time[29:35], layout = c(1, 7)), split = c(1, 1, 1, 2)) plot(update(ssc.time[29:35], layout = c(1, 7)), split = c(1, 2, 1, 2), newpage = FALSE) ## scatter plot matrix of individual flowFrames splom(GvHD[["s10a07"]], smooth = FALSE) splom(GvHD[["s10a07"]], smooth = FALSE, prepanel.limits = function(x) quantile(as.numeric(x), c(0.0, 0.99))) ## time plot of individual flowFrames xyplot(GvHD[["s5a07"]], time = "Time") xyplot(`FSC-H` + `SSC-H` + `FL1-H` ~ Time, GvHD[["s5a07"]], aspect = "xy", outer = TRUE, scales = list(y = "free"), type = "l", smooth = FALSE) ## a bivariate scatterplot xyplot(`FSC-H` ~ `SSC-H`, GvHD[["s5a01"]], nbin = 100) ## displaying filters n2gate <- norm2Filter("SSC-H", "FSC-H") xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data = GvHD, filter=n2gate, layout=c(7, 5)) xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data=transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD, smooth=FALSE, filter=n2gate, layout=c(7, 5)) xyplot(`SSC-H` ~ `FSC-H` | Patient:Visit, data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD, subset = Patient == "6", filter = rectangleGate("FSC-H"=c(5.5, 7),"SSC-H"=c(4, 6.5))) n2gate.results <- filter(GvHD, n2gate) xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, subset=Patient == "6", filter=n2gate.results, smooth=FALSE) xyplot(`SSC-H` ~ `FSC-H` | Visit, data = GvHD, subset = Patient == "6", smooth = FALSE, filter = n2gate, filterResults = n2gate.results, displayFilter = list(lwd = 0.5))