enrich_bar_plot: enrich_bar_plot

In tidymass/metpath: Pathway analysis for metabolomics data

enrich_bar_plot

Description

Bar plot for enrich_result

Usage

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
)

Arguments

object	enrich_result object.
x_axis	"p_value_adjust or "p_value"
cutoff	cutoff for p_value_adjust or p_value.
top	top pathways to show.
axis.text.x.width	axis.text.x.width
axis.text.y.width	axis.text.y.width

Author(s)

Xiaotao Shen [e-mail]

Examples

## Not run: 
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
  )

## End(Not run)

tidymass/metpath documentation built on July 21, 2023, 3:11 p.m.