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 1.6.11 Index]