plot.flowPeaks {flowPeaks} | R Documentation

## Plot the results generated by flowPeaks

### Description

This function takes the results generated from flowPeaks as an input, and plot the data in 2D. These plots display the clustering structure

### Usage

    ## S3 method for class 'flowPeaks'
    plot(x,idx=c(1,2),drawlab=FALSE,
    cols=c("red","green3","blue","cyan","magenta","yellow","gray"),drawvor=TRUE,
                             drawlocalpeaks=FALSE,drawkmeans=TRUE,drawboundary=TRUE,
                             classlab, negcol, negpch,...)

### Arguments

`x` | Anobject of class flowPeaks, e.g., t the output from the functions `flowPeaks` or `adjust.flowPeaks`
`idx` | The index of the columns will be used to plot the clustering. idx needs to be at least legnth 2, and have no duplicate elements, and the values can only take from 1 to d, where d is the number of columns for the input matrix x that is used as an input of the function flowPeaks
`drawlab` | The option to decide whether we should draw the cluster labels
`cols` | The color specification for plotting the points in each cluster. Please note, "white" and "black" are not allowed, which are reserved for other purpse
`drawvor` | Deciding whether the voronoi diagram should be drawn, only good for 2D data
`drawlocalpeaks` | Decding whether the local peaks with a triangle symbol should be drawn
`drawkmeans` | Deciding whether the kmeans center with a filled circle should be drawn
`drawboundary` | Deciding whether the boudary between clusters should be drawn, only good for 2D data
`classlab` | Use this to replace the default class labels from x$peak.cluster, for example, the classlab may come from `assign.flowPeaks`
`negcol` | Deciding the color of the negative, which are outliers
`negpch` | Deciing the symbols for the outliers
`...` | Optional additional arguments. At present no additional arguments are used.

### Author(s)

Yongchao Ge yongchao.ge@gmail.com

### See Also

`flowPeaks`

[Package flowPeaks version 1.36.0 Index]