draw_volcano_plot {transite} | R Documentation

## k-mer Enrichment Volcano Plot

### Description

Uses a volcano plot to visualize k-mer enrichment. X-axis is \log_2 enrichment value, y-axis is \log_10 significance, i.e., multiple testing corrected p-value from Fisher's exact test or Pearson's chi-squared test.

### Usage

    draw_volcano_plot(
      kmers,
      motif_kmers,
      motif_rbps,
      significance_threshold = 0.01,
      show_legend = TRUE
    )

### Arguments

`kmers` | data frame with the following columns: kmer, adj_p_value, enrichment
`motif_kmers` | set of k-mers that are associated with a certain motif, will be highlighted in volcano plot
`motif_rbps` | name of RNA-binding proteins associated with highlighted k-mers (character vector of length 1)
`significance_threshold` | p-value threshold for significance, e.g., `0.05` or `0.01`
`show_legend` | whether or not a legend should be shown

### Value

volcano plot

### See Also

Other TSMA functions: `run_kmer_tsma()`, `run_matrix_tsma()`

Other k-mer functions: `calculate_kmer_enrichment()`, `check_kmers()`, `compute_kmer_enrichment()`, `count_homopolymer_corrected_kmers()`, `estimate_significance_core()`, `estimate_significance()`, `generate_kmers()`, `generate_permuted_enrichments()`, `run_kmer_spma()`, `run_kmer_tsma()`

### Examples

    motif <- get_motif_by_id("951_12324455")
    draw_volcano_plot(transite:::kmers_enrichment, get_hexamers(motif[[1]]),
      get_rbps(motif[[1]]))

    ## Not run:
    foreground_set <- c("UGUGGG", "GUGGGG", "GUGUGG", "UGUGGU")
    background_set <- unique(c(foreground_set, c(
      "CAACAGCCUUAAUU", "CAGUCAAGACUCC", "CUUUGGGGAAU",
      "UCAUUUUAUUAAA", "AAUUGGUGUCUGGAUACUUCCCUGUACAU",
      "AUCAAAUUA", "AGAU", "GACACUUAAAGAUCCU",
      "UAGCAUUAACUUAAUG", "AUGGA", "GAAGAGUGCUCA",
      "AUAGAC", "AGUUC", "CCAGUAA",
      "CCACACAC", "CUCAUUGGAG", "ACUUUCCCACA", "CAGGUCAGCA",
      "CCACACCAG", "CCACACAUCAGU", "CACACACUCC", "CAGCCCCCCACAGGCA"
    )))

    motif <- get_motif_by_id("M178_0.6")
    results <- run_kmer_tsma(list(foreground_set), background_set,
                           motifs = motif)
    draw_volcano_plot(results[[1]]$motif_kmers_dfs[[1]],
        get_hexamers(motif[[1]]), "test RBP")
    ## End(Not run)

[Package transite version 1.10.0 Index]