draw_volcano_plot | 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()
,
create_kmer_origin_list()
,
estimate_significance()
,
estimate_significance_core()
,
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)
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