densityPlot {MetaCyto} | R Documentation

## Draw density plot for each cell cluster.

### Description

A function that draws density plot for each cell cluster.

### Usage

    densityPlot(fcsFrame, clusterList, cutoff, markerToPlot = NULL)

### Arguments

`fcsFrame` | A flow Frame object returned from preprocessing function.
`clusterList` | A list, each element should be a vector containing the IDs of all cells that belong to a cluster
`cutoff` | A vector of cutoff values to bisect the distribution of each marker. The names of the vector should be the same as the marker names.
`markerToPlot` | A vector specifying markers included in the plot. If NULL, all markers will be plotted.

### Details

The plot can be very large, we suggest plotting it into a pdf jpeg file directly.

### Value

NULL. The plot will show up automatically.

### Examples

    # Find fcs files
    files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
                      package="MetaCyto")
    files=list.files(files,pattern="fcs$",full.names=TRUE)
    # Preprocess
    fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)
    # Search clusters
    cluster_list=searchCluster(fcsFrame=fcs,
                               clusterLabel=c("CD3+|CD8+","CD3-|CD19+"))
    # plot density plot for clusters
    densityPlot(fcs,
                clusterList=cluster_list$clusterList,
                cutoff=cluster_list$cutoff,
                markerToPlot=c("CD3","CD8","CD19"))

[Package MetaCyto version 1.12.0 Index]