draw_volcano_plot {transite} | R Documentation |
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.
draw_volcano_plot( kmers, motif_kmers, motif_rbps, significance_threshold = 0.01, show_legend = TRUE )
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., |
show_legend |
whether or not a legend should be shown |
volcano plot
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()
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)