plot_similarity {CEMiTool}R Documentation

Plot study module similarity

Description

Plot study module similarity

Usage

plot_similarity(mod_stats, weight_col = "logfdr")

Arguments

mod_stats

List output from function stat_overlap_mods

weight_col

Character string denoting the weighting column for module similarity. One of "Jaccard", "Fisherp", "fdr", "logp" or "logfdr". Default: "logfdr".

Value

A plot showing the similarity between study modules

Examples

## Not run: 
# Run the cemitool function five times on expr0 dataset. Each time, 10 samples will be removed.
data(expr0)
data(sample_annot)
set.seed(10)
dset1 <- expr0[,-sample(1:ncol(expr0), 10)]
set.seed(11)
dset2 <- expr0[,-sample(1:ncol(expr0), 10)]
set.seed(12)
dset3 <- expr0[,-sample(1:ncol(expr0), 10)]
set.seed(13)
dset4 <- expr0[,-sample(1:ncol(expr0), 10)]
set.seed(14)
dset5 <- expr0[,-sample(1:ncol(expr0), 10)]

cem1 <- cemitool(dset1, sample_annot, plot=FALSE) 
cem2 <- cemitool(dset2, sample_annot, plot=FALSE)
cem3 <- cemitool(dset3, sample_annot, plot=FALSE) 
cem4 <- cemitool(dset4, sample_annot, plot=FALSE) 
cem5 <- cemitool(dset5, sample_annot, plot=FALSE) 
mod_stats <- stat_overlap_mods(list(cem1, cem2, cem3, cem4, cem5), comp_group="g0")
plot_similarity(mod_stats)

## End(Not run)

[Package CEMiTool version 1.8.0 Index]