draw_volcano_plot: _k_-mer Enrichment Volcano Plot

In kkrismer/transite: RNA-binding protein motif analysis

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(), create_kmer_origin_list(), estimate_significance(), estimate_significance_core(), 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)

kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.