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]