meta.plot {immunoClust} | R Documentation |
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.
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)
meta |
The list-object returned by the function meta.process. |
exp |
The vector of |
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 |
png_pre |
Same as |
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. |
Plots the clustering results on an appropriatei plotting device or png-file.
Uses the scatter-clustering results of the meta object.
Short-cut for plotting the meta-clustering results.
Short-cut for plotting the scatter-clustering result.
Plots the meta-clustering results in one hierachy level and iterates through the sub-levels of the gate.
Plots the meta-clustering gating results in each
hierarchy level stored in png-files in the directory given by pre
.
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
.
Plots the cell-events belonging the
meta-clusters in include
for each sample used for meta-clustering
in a separate file.
Till Sörensen till-antoni.soerensen@charite.de
data(dat.meta) meta.plotClusters(dat.meta)