lattice-methods {flowViz} | R Documentation

## Methods implementing Lattice displays for flow data

### Description

Various methods implementing multipanel visualizations for flow data using infrastructure provided in the lattice package. The original generics for these methods are defined in lattice, and these S4 methods (mostly) dispatch on a formula and the `data` argument which must be of class `flowSet` or `flowFrame`. The formula has to be fairly basic: conditioning can be done using phenodata variables and channel names (the `colnames` slot) can be used as panel variables. In the case of the `densityplot` method, a phenodata variable must be used on the left hand side of the formula as a panel variable to stack the densities. See examples below for sample usage.

### Usage

    ## methods for 'flowSet' objects

    ## S4 method for signature 'formula, flowSet':
    densityplot(x, data,
                xlab, as.table = TRUE, overlap = 0.3,
                prepanel = prepanel.densityplot.flowset,
                panel = panel.densityplot.flowset,
                ...)

    ## S4 method for signature 'formula, flowSet':
    qqmath(x, data, xlab, ylab,
           f.value = function(n) ppoints(ceiling(sqrt(n))),
           distribution = qnorm, ...)

    ## S4 method for signature 'formula, flowSet':
    levelplot(x, data, xlab, ylab,
              as.table = TRUE, contour = TRUE, labels = FALSE,
              n = 50, ...)

    ## methods for 'flowFrame' objects

    ## S4 method for signature 'flowFrame, missing':
    parallel(x, data,
             reorder.by = function(x) var(x, na.rm = TRUE),
             time = "Time", exclude.time = TRUE,
             ...)

### Arguments

`x` | a formula describing the structure of the plot and the variables to be used in the display.
`data` | a `flowSet` object that serves as a source of data
`xlab, ylab` | Labels for data axes, with suitable defaults taken from the formula
`overlap` | the amount of overlap between stacked density plots
`prepanel` | the prepanel function. See `xyplot`
`panel` | the panel function. See `xyplot`
`f.value, distribution` | number of points used in Q-Q plot, and the reference distribution used. See `qqmath` for details.
`n` | the number of bins on each axis to be used when evaluating the density
`as.table, contour, labels` | 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.
`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 or parallel coordinates plot. It is rarely meaningful not to do so.
`reorder.by` | a function, which is applied to each column. The columns are ordered by the results. Reordering can be suppressed by setting this to `NULL`.
`...` | more arguments, usually passed on to the underlying lattice methods.

### Details

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 (Trellis docs would also work for the fundamentals).

### Methods

densityplot
  `signature(x = "formula", data = "flowSet")`: creates density plots for a given channel, with samples stacked according to a phenodata variable. Colors are used to indicate common values of this covariate across panels.
qqmath
  `signature(x = "formula", data = "flowSet")`: creates theoretical quantile plots of a given channel, with one or more samples per panel
levelplot
  `signature(x = "formula", data = "flowSet")`: similar to the `xyplot` method, but plots estimated density (using `kde2d`) with a common z-scale and an optional color key.
parallel
  `signature(x = "flowFrame", data = "missing")`: draws a parallel coordinates plot of all channels (excluding time, by default) of a `flowFrame` object. This is rarely useful without transparency, but that is currently only possible with the `pdf` device (and perhaps the aqua device as well).

### Examples

    data(GvHD)

    densityplot(Visit ~ `FSC-H` | Patient, GvHD)

    densityplot(Visit ~ asinh(`FSC-H`) | Patient, GvHD,
                panel = function(...) {
                    ylim <- current.panel.limits()$ylim
                    v <- c(5.5, 7)
                    panel.rect(v[1], ylim[1],
                               v[2], ylim[2],
                               col = "grey")
                    panel.densityplot.flowset(...)
                })

    qqmath( ~ `FSC-H` | factor(Patient), GvHD,
           grid = TRUE, type = "l",
           f.value = ppoints(100))

    ## contourplot of bivariate density:

    require(colorspace)
    YlOrBr <- c("#FFFFD4", "#FED98E", "#FE9929", "#D95F0E", "#993404")
    colori <- colorRampPalette(YlOrBr)
    levelplot(asinh(`SSC-H`) ~ asinh(`FSC-H`) | Visit + Patient, GvHD, n = 20,
              col.regions = colori(50), main = "Contour Plot")

    ## parallel coordinate plots

    parallel(GvHD[["s6a01"]])

    ## Not run:

    ## try with PDF device
    parallel(GvHD[["s7a01"]], alpha = 0.01)

    ## End(Not run)

[Package flowViz version 1.2.0 Index]