meta.plot {immunoClust} | R Documentation

## Ploting of immunoClust Meta-clustering Results

### Description

Thess functions collect plotting helper routinest of the results `meta.process` and relies on the prelimary gating which is also included with the meta.process function.

### Usage

    meta.plotClustersForScatter(meta, include, filter=0)

    meta.plotClusters( meta, include=c() )

    meta.plotScatter(meta)

    meta.plotGate(meta, gating, pre, gates, pattern=c(),
    png.size=1024, filter=0)

    meta.plotGating(meta, pre, pattern=c(), png.size=1024, filter=0)

    meta.plotExpResult(meta, exp, pattern=c(), png_pre, plot.ellipse=FALSE,
    plot.class=FALSE, png.size=1024, filter=0, ellipse.quantile=0.95)

    meta.plotExpClusters(meta, exp, include=c(), png_pre, png.size=1024,
    plot.ellipse=FALSE, plot.class=FALSE, class.col=c(), filter=0,
    ellipse.quantile=0.95, desc=NULL, N=NULL)

### Arguments

`meta` | The list-object returned by the function meta.process.
`exp` | The vector of `immunoClust-objects` used for meta-clustering.
`include` | A numeric vector specifying which clusters will be shown on the plot. By default, all clusters are included.
`pattern` | A character array which give the decription path for the gate to be plotted.
`gating` | A list object containing the hierarchical gating information as generated within the meta-clustering process of immunoCust.
`pre` | File prefix for the output png image files. The name for the png-file is generated by concatinating `pre` with the description of the gate.
`png_pre` | Same as `pre` (see above).
`png.size` | Pixel width and height for the output the png image files.
`plot.ellipse` | A logical value indicating whether the cluster 90% percentil boundary is to be drawn or not.
`ellipse.quantile` | Quantile value for the clusters boundary ellipsis.
`plot.class` | Indicating whether the plotted cell-clusters are colored by the meta-clusters or individually.
`class.col` | Color(s) of the plotting cell-clusters. May specify a different color for each cluster.
`desc` | A character vector for the parameter description.
`N` | An integer for the maximum number of observations to be plotted. By default all observations are plotted.
`filter` | A numeric number to filter out meta-clusters which have less number of cell-clusters.
`gates` | An optional numeric matrix with the gate positions in each parameter.

### Value

Plots the clustering results on an appropriatei plotting device or png-file.

meta.plotClustersForScatter

  Uses the scatter-clustering results of the meta object.

meta.plotClusters

  Short-cut for plotting the meta-clustering results.

meta.plotScatter

  Short-cut for plotting the scatter-clustering result.

meta.plotGate

  Plots the meta-clustering results in one hierachy level and iterates through the sub-levels of the gate.

meta.plotGating

  Plots the meta-clustering gating results in each hierarchy level stored in png-files in the directory given by `pre`.

meta.plotExpResults

  Plots the the cell-events belonginig to meta-clusters within a gate for each sample in a separate file. The gate is specified by `pattern`.

meta.plotExpClusters

  Plots the cell-events belonging the meta-clusters in `include` for each sample used for meta-clustering in a separate file.

### Author(s)

Till Sörensen till-antoni.soerensen@charite.de

### See Also

`meta.process`

### Examples

    data(dat.meta)
    meta.plotClusters(dat.meta)

[Package immunoClust version 1.12.0 Index]