plot_similarity {CEMiTool} | R Documentation |
Plot study module similarity
plot_similarity(mod_stats, weight_col = "logfdr")
mod_stats |
List output from function |
weight_col |
Character string denoting the weighting column for module similarity. One of "Jaccard", "Fisherp", "fdr", "logp" or "logfdr". Default: "logfdr". |
A plot showing the similarity between study modules
## 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)