Question: How to extract plots from ConsensusClusterPlus package
0
gravatar for manali.rupji
3.2 years ago by
manali.rupji20
United States
manali.rupji20 wrote:

Hello All,

Is there a way to extract the plots separately from the ConsensusClusterPlus package? For example, using the example data from the package, I can print the last three plots as below,

library(ALL)
data(ALL)
d=exprs(ALL)

mads=apply(d,1,mad)
d=d[rev(order(mads))[1:5000],]

d = sweep(d,1, apply(d,1,median,na.rm=T))

library(ConsensusClusterPlus)

par(mfrow=c(1,3))
title=tempdir()
results = ConsensusClusterPlus(d,maxK=6,reps=50,pItem=0.8,pFeature=1,
                               title=title,clusterAlg="hc",distance="pearson",seed=1262118388.71279)

But, I wish to extract the consensus heatmap (say plot #2 which represents the optimal number of clusters) from the results and display separately.

Any help in this regard would be very helpful.

Thanks in advance, M

plots consensusclusterplus • 2.7k views
ADD COMMENTlink modified 3 months ago by federico.nichetti0 • written 3.2 years ago by manali.rupji20

Hey,

Why do not use plot="pdf" in ConsensusClusterPlus function, so you will get 6 individual plots for each number of cluster, later you can take interest of yours.

results = ConsensusClusterPlus(d,maxK=6,reps=50,pItem=0.8,pFeature=1,
                           title=title,clusterAlg="hc",distance="pearson",seed=1262118388.71279, plot="pdf")
ADD REPLYlink written 3.2 years ago by arta620

Hi there, I'm trying the ConsensusClusterPlus package, but I can't view the plots that it generates. Can you help? Thanks!

ADD REPLYlink written 3 months ago by federico.nichetti0
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