Plot intensity distribution of metabolite across conditions

Usage

compare_metabo_distr(obj, metabolite, conds_of_interest = NULL)

Arguments

obj: A S2IsoMEr object after enrichment analysis.
metabolite: A character indicating metabolite name
conds_of_interest: Optional. A character vector specifying which conditions to include in the plot. If NULL (the default), all conditions are included.

Value

A ggplot2 object displaying the density plot of metabolite intensities across conditions.

Examples

if (FALSE) { # \dontrun{
data("example_ORA_obj")
data("example_ORA_custom_universe")
input_scm = example_ORA_obj$scmatrix
conds = example_ORA_obj$conditions
cond_x = "U"
cond_y = "F"
ORA_obj <- initEnrichment(
  scmatrix = input_scm,
  conditions = conds,
  enrichment_type = "ORA",
  annot_db = "HMDB",
  consider_isomers = TRUE,
  consider_isobars = TRUE,
  polarization_mode = "positive",
  background_type = "sub_class",
  molecule_type = "Metabo",
  condition.x = cond_x,
  condition.y = cond_y
)
ORA_res <- Run_enrichment(
  object = ORA_obj,
  custom_universe = example_ORA_custom_universe,
  report_ambiguity_scores = TRUE,
  DE_LFC_cutoff = 0,
  min.pct.diff = 0
)
TP_ions = get_TP_markers_per_Term(ORA_boot_df = ORA_res$downregulated$unfiltered_enrich_res,
                                 term_of_interest = "Glycerophosphocholines")
TP_ions = map_TP_markers_to_ions(markers = TP_ions,scm_ions = rownames(input_scm))
p = compare_metabo_distr(ORA_obj, metabolite = TP_ions[5],
                         conds_of_interest = c(cond_x, cond_y))
} # }