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, filterResults = NULL, displayFilter = TRUE, ...) ## 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.xyplot.flowset(x, frames, channel.x, channel.y, channel.x.name, channel.y.name, filter = NULL, filterResults = NULL, displayFilter = TRUE, pch, smooth, ...) prepanel.xyplot.flowset(x, frames, channel.x, channel.y, ...)
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 ,
names of flow frames. |
data |
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.
|
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. |
prepanel |
the prepanel function. See
xyplot |
panel |
the panel function. See
xyplot |
filter |
A filter object. Ignored
when filterResults is not NULL . |
filterResults |
A
filterResult object, that
is the result of applying a filter on each frame in data . If
this is NULL but filter is not, it will be created on
the fly by applying filter to each frame. |
displayFilter |
logical or list. If TRUE , an attempt is
made to display the geometric boundaries of filter (if
specified) in the plot. The same holds if displayFilter is a
list, but in that case the components are interpreted as graphical
parameters to be passed on to
panel.polygon
|
time |
A character string giving the name of the column recording time. |
exclude.time |
logical, specifying whether to exclude the time variable from a scatter plot matrix. |
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. |
frames |
an environment containing frame-specific data |
... |
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 = "l", 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) 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, ## displayFilter = TRUE, 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, ## displayFilter = list(border = "black"), 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)), displayFilter = list(lwd = 3)) n2gate.results <- filter(GvHD, n2gate %on% transform("SSC-H"=asinh,"FSC-H"=asinh)) xyplot(`SSC-H` ~ `FSC-H` | Visit, data = GvHD, subset = Patient == "6", filterResults = 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)) xyplot(`SSC-H` ~ `FSC-H` | Visit, data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD, subset = Patient == "6", smooth = FALSE, filter = rectangleGate("FSC-H"=c(5.5, 7),"SSC-H"=c(4, 6.5)), filterResults = n2gate.results, displayFilter = list(border = 'red'))