ConsensusMatPlot: A function to create image plot of the consensus matrix

In IntNMF: Integrative Clustering of Multiple Genomic Dataset

Description

Given the integrative NMF fit object, the function creates image plot of the consensus matrix ordered according to clusters groups. Cleaner block structure indicates stronger clusters.

Usage

ConsensusMatPlot(fit, rowLab = TRUE, colLab = TRUE)

Arguments

fit	A nmf.mnnals fit object
rowLab	If true row label is displayed. Default is TRUE.
colLab	If true column label is displayed. Default is TRUE.

Value

Image plot of the consensus matrix ordered according to cluster groups is returned.

Author(s)

Prabhakar Chalise, Rama Raghavan, Brooke Fridley

References

Brunnet J, Tamayo P Golub, T and Mesirov J (2004) Metagene and molecular pattern discovery using matrix factorization. PNAS, 101, 4164-4169

Monti S, Tamayo P, Mesirov J and Golup T (2003). Consesus Clustering: A resampling based method for class discovery and visualization of gene expression microarray data. Machine Learning J, 52:91-118.

Examples

prop <- c(0.20,0.30,0.27,0.23)
effect <- 2.5
sim.D <- InterSIM(n.sample=100,cluster.sample.prop=prop,delta.methyl=effect,
delta.expr=effect,delta.protein=effect,p.DMP=0.25,p.DEG=NULL,p.DEP=NULL,
do.plot=FALSE, sample.cluster=TRUE, feature.cluster=TRUE)
dat1 <- sim.D$dat.methyl
dat2 <- sim.D$dat.expr
dat3 <- sim.D$dat.protein
true.cluster.assignment <- sim.D$clustering.assignment

## Make all data positive by shifting to positive direction.
## Also rescale the datasets so that they are comparable.
if (!all(dat1>=0)) dat1 <- pmax(dat1 + abs(min(dat1)), .Machine$double.eps)
dat1 <- dat1/max(dat1)
if (!all(dat2>=0)) dat2 <- pmax(dat2 + abs(min(dat2)), .Machine$double.eps)
dat2 <- dat2/max(dat2)
if (!all(dat3>=0)) dat3 <- pmax(dat3 + abs(min(dat3)), .Machine$double.eps)
dat3 <- dat3/max(dat3)

# The function nmf.mnnals requires the samples to be on rows and variables on columns.
dat <- list(dat1,dat2,dat3)
fit <- nmf.mnnals(dat=dat,k=length(prop),maxiter=200,st.count=20,n.ini=15,ini.nndsvd=TRUE,
seed=TRUE)
ConsensusMatPlot(fit,rowLab=TRUE,colLab=TRUE)

Example output

Loading required package: MASS
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2
Loading required package: mclust
Package 'mclust' version 5.4.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: InterSIM
Loading required package: tools
There were 18 warnings (use warnings() to see them)

IntNMF documentation built on May 1, 2019, 6:35 p.m.