Bar plot for enrich_result
enrich_bar_plot(
object,
x_axis = c("p_value_adjust", "p_value"),
cutoff = 0.05,
top = 10,
axis.text.x.width = 15,
axis.text.y.width = 15
)enrich_result object.
"p_value_adjust or "p_value"
cutoff for p_value_adjust or p_value.
top pathways to show.
axis.text.x.width
axis.text.y.width
if (FALSE) {
data("kegg_hsa_pathway")
remain_idx =
kegg_hsa_pathway@pathway_class %>%
unlist() %>%
stringr::str_detect("Disease") %>%
`!`() %>%
which()
pathway_database =
filter_pathway(object = kegg_hsa_pathway,
remain_idx = remain_idx[1:50])
data("query_id_kegg")
kegg_enrichment =
enrich_kegg(
query_id = query_id_kegg,
query_type = "compound",
id_type = "KEGG",
pathway_database = pathway_database,
p_cutoff = 0.05,
p_adjust_method = "BH",
method = "hypergeometric",
threads = 5
)
}