densityplot {flowViz} | R Documentation

## One-dimensional density plots for flow data

### Description

So far, density plots are only implemented for `flowSet`. The idea is to horizontally stack plots of density estimates for all frames in the `flowSet` for one or several flow parameters. In the latter case, each parameter will be plotted in a separate panel, i.e., we implicitely condition on parameters.

### Usage

    ## method 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,
        filter=NULL,
        scales=list(y=list(draw=F)),
        channels,
        ...)

    prepanel.densityplot.flowset(
        x,
        y,
        darg=list(n=50, na.rm=TRUE),
        frames,
        overlap=0.3,
        subscripts,
        ...,
        which.channel)

    panel.densityplot.flowset(
        x,
        y,
        darg=list(n=50, na.rm=TRUE),
        frames,
        channel,
        overlap = 0.3,
        channel.name,
        filter=NULL,
        fill=superpose.polygon$col,
        lty=superpose.polygon$lty,
        lwd=superpose.polygon$lwd,
        alpha=superpose.polygon$alpha,
        col=superpose.polygon$border,
        groups=NULL,
        refline=NULL,
        gpar,
        ...)

    ## methods for various workflow objects
    ## S4 method for signature 'formula, view':
    densityplot(
        x,
        data,
        ...)

    ## S4 method for signature 'view, missing':
    densityplot(
        x,
        data,
        channels,
        ...)

### Arguments

`x` | A formula describing the structure of the plot and the variables to be used in the display. The structure of the formula is `factor ~ parameter`, where `factor` can be any of the phenotypic factors in the `phenoData` slot or an appropriate factor object and `parameter` is a flow parameter. Panels for multiple parameters are drawn if the formula structure is similar to `factor ~ parameter1 + parameter2`, and `factor` can be missing, in which case the sample names are used as y-variable. To facilitate programatic access, the formula can be of special structure `factor ~ .`, in which case the optional `channel` argument is considered for parameter selection. For the workflow methods, `x` can also be one of the several workflow objects.
`data` | A `flowSet` object that serves as a source of data, either a `flowFrame` or `flowSet`, or one of the several workflow objects.
`xlab` | Label for data x axis, with suitable defaults taken from the formula
`as.table, scales, darg` | 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. `darg` gets passed on to `density`.
`overlap` | The amount of overlap between stacked density plots
`prepanel` | The prepanel function. See `xyplot`
`panel` | the panel function. See `xyplot`
`filter` | A `filter`, `filterResult` or `filterResultList` object or a list of such objects of the same length as the `flowSet`. If applicable, the gate region will be superiposed on the density curves using color shading. The software will figure out whether the `filter` needs to be evaluated in order to be plotted (in which case providing a `filterResult` can speed things up considerably).
`channels` | A character vector of parameters that are supposed to be plotted when the formula in `x` is of structure `factor ~ .`.
`subscripts, which.channel, channel.name, y` | Internal indices necessary to map panels to parameters.
`frames` | An environment containing frame-specific data.
`channel` | The name of the currently plotted flow parameter.
`col, fill, lty, lwd, alpha` | Graphical parameters. These mostly exist for conveniance and much more control is available throught the `lattice`-like `par.setting` and `flowViz.par.set` customization. The relevant parameter category for density plots is `gate.density` with available parameters `col, \code{fill}, \code{lwd} \code{alpha} and \code{lty}`. See `flowViz.par.set` for details.
`groups` | Use identical colors for grouping. The value of the argument is expected to be a phenotypic variable in the `flowSet`.
`refline` | Add one ore more vertical reference lines to the plot. This argument is directly passed to `panel.abline`.
`gpar` | A list of graphical parameters that are passed down to the low level panel functions. This is for internal use only. The public user interface to set graphical parameters is either `par.settings` for customization of a single call or `flowViz.par.set` for customization of session-wide defaults.
`...` | 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 one or several channels, with samples stacked according to a `phenoData` variable. Colors are used to indicate common values of this covariate across panels. Filters can be added as the optional `filter` arguments. See `xyplot` for details.
densityplot
  `signature(x = "formula", data = "view")`: A method to create density plots for workspace `view` objects. This still allows for some level of customization, but most defaults will be set depending on the input object.
densityplot
  `signature(x = "view", data = "missing")`: The default method for view objects. All defaults will be set.

### Examples

    data(GvHD)
    GvHD <- GvHD[pData(GvHD)$Patient %in% 6:7]

    densityplot(~ `FSC-H`, GvHD)

    densityplot(~ `FSC-H` + `SSC-H`, GvHD)

    densityplot(~ ., GvHD[1:3])

    ## include a filter
    densityplot(~ `FSC-H`, GvHD, filter=curv1Filter("FSC-H"))

[Package flowViz version 1.8.0 Index]