ChooseCluster: Interactive plot to determine DE Genes and DE features for a...

In MosaiClusteR: An Umbrella Framework for Multi-Source and Multi-Omics Clustering

Interactive plot to determine DE Genes and DE features for a specific cluster

Description

If desired, the function produces a dendrogram of a clustering result. One or multiple clusters can be indicated by a mouse click. From these clusters DE genes and characteristic features are determined. It is also possible to provide the objects of interest without producing the plot.

Usage

ChooseCluster(
  Interactive = TRUE,
  leadCpds = NULL,
  clusterResult = NULL,
  colorLab = NULL,
  binData = NULL,
  contData = NULL,
  datanames = c("FP"),
  geneExpr = NULL,
  topChar = 20,
  topG = 20,
  sign = 0.05,
  nrclusters = NULL,
  cols = NULL,
  n = 1
)

Arguments

Interactive	Logical. Whether an interactive plot should be made. Defaults to TRUE.
leadCpds	A list of the objects of the clusters of interest. Defaults to NULL.
clusterResult	The output of one of the aggregated cluster functions. Default is NULL.
colorLab	The clustering result the dendrogram should be colored after. Default is NULL.
binData	A list of the binary feature data matrices. Default is NULL.
contData	A list of continuous data sets of the objects. Default is NULL.
datanames	A vector with the names of the data matrices. Default is c("FP").
geneExpr	A gene expression matrix, may also be an ExpressionSet. Default is NULL.
topChar	The number of top characteristics to return. Default is 20.
topG	The number of top genes to return. Default is 20.
sign	The significance level. Default is 0.05.
nrclusters	Optional. The number of clusters to cut the dendrogram in. Default is NULL.
cols	The colors to use in the dendrogram. Default is NULL.
n	The number of clusters one wants to identify by a mouse click. Default is 1.

Details

This function may require the suggested packages 'a4Base', 'a4Core' and 'limma' when a gene expression matrix is supplied.

Value

A list with one element per cluster of interest with elements objects, Characteristics and (optionally) Genes.

Examples

## Not run: 
data(fingerprintMat)
data(targetMat)
data(geneMat)

MCF7_F = Cluster(fingerprintMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)
MCF7_T = Cluster(targetMat,type="data",distmeasure="tanimoto",normalize=FALSE,
method=NULL,clust="agnes",linkage="flexible",gap=FALSE,maxK=55,StopRange=FALSE)

MCF7_Interactive=ChooseCluster(Interactive=TRUE,leadCpds=NULL,clusterResult=MCF7_T,
colorLab=MCF7_F,binData=list(fingerprintMat),datanames=c("FP"),geneExpr=geneMat,
topChar = 20, topG = 20,nrclusters=7,n=1)

## End(Not run)

MosaiClusteR documentation built on Oct. 25, 2026, 1:08 a.m.