flowMeans: flowMeans

In flowMeans: Non-parametric Flow Cytometry Data Gating

Description

Finds a good fit to the data using k-means clustering algorithm. Then merges the adjacent dense spherical clusters to find non-spherical clusters.

Usage

flowMeans(x, varNames=NULL, MaxN = NA, NumC = NA, iter.max = 50, nstart = 10,
Mahalanobis = TRUE, Standardize = TRUE, Update = "Mahalanobis", OrthagonalResiduals=TRUE,
MaxCovN=NA, MaxKernN=NA, addNoise=TRUE)

Arguments

x	A matrix, data frame of observations, or object of class flowFrame. Rows correspond to observations and columns correspond to variables.
varNames	A character vector specifying the variables (columns) to be included in clustering. When it is left unspecified, all the variables will be used.
MaxN	Maximum number of clusters. If set to NA (default) the value will be estimated automatically.
NumC	Number of clusters. If set to NA (default) the value will be estimated automatically.
iter.max	The maximum number of iterations allowed.
nstart	The number of random sets used for initialization.
Mahalanobis	Boolean value. If TRUE (default) mahalanobis distance will be used. Otherwised, euclidean distance will be used.
Standardize	Boolean value. If TRUE (default) the data will be transformed to the [0,1] interval.
Update	String value. If set to "Mahalanobis" the distance function will be updated at each merging iteration with recalculating mahalanobis distances. If set to "Mean" the distance matrix will be updated after each merging step with averaging. If set to "None" the distance matrix will not be updated.
MaxCovN	Maximum number of points, used for calculating the covariance. If set to NA (default), all the points will be used.)
MaxKernN	Maximum number of points, used for counting the modes using kernel density estimation. If set to NA (default), all the points will be used.)
addNoise	Boolean value. Determines if uniform noise must be added to the data to prevent singularity issues or not.
OrthagonalResiduals	Boolean value, indicates if the residuals must be transformed to orthagonal distance or not.

Details

If Mahalanobis distance is not used (i.e., Mahalanobis=FALSE) then the Update value cannot be set to Mahalanobis (i.e., Update="Mahalanobis")

Value

Label	A vector of integers indicating the cluster to which each point is allocated.
Labels	A list of vectors of integers indicating the cluster to which each point is allocated at each merging iteration.
Mats	A list of distance matrixes between clusters at every merging iteration.
MaxN	Maximum number of clusters
Mins	A vector of integers indicating the distance between the two clusters chosen to be merged at every iteration.
MinIndex	Index of the merging step that produced the final results.
Line1	First regression line used for finding the changepoint for stopping the merging process.
Line2	Second regression line used for finding the changepoint for stopping the merging process.

Author(s)

Nima Aghaeepour

Examples

library(flowMeans)
data(x)
res <- flowMeans(x, c("FL1.H", "FL2.H", "FL3.H", "FL4.H"), MaxN=10)
plot(x[,c(3,4)], res, c("FL1.H", "FL2.H"))

Example output

Warning messages:
1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
2: 'rgl_init' failed, running with rgl.useNULL = TRUE 
3: .onUnload failed in unloadNamespace() for 'rgl', details:
  call: fun(...)
  error: object 'rgl_quit' not found 
4: no DISPLAY variable so Tk is not available 

flowMeans documentation built on Nov. 8, 2020, 4:51 p.m.