plot_features_box function

Plot features boxplot

plot_features_box(
  kodf,
  group = NULL,
  metadata = NULL,
  map_id = "map00780",
  select_ko = NULL,
  only_sig = FALSE,
  box_param = NULL,
  modulelist = NULL,
  KO_description = FALSE,
  str_width = 50
)

Arguments

• kodf: KO_abundance table, rowname is ko id (e.g. K00001),colnames is samples. or result of get_reporter_score
• group: The compare group (two category) in your data, one column name of metadata when metadata exist or a vector whose length equal to columns number of kodf.
• metadata: metadata
• map_id: the pathway or module id
• select_ko: select which ko
• only_sig: only show the significant features
• box_param: parameters pass to group_box
• modulelist: NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the KOlist as example, use custom_modulelist.
• KO_description: show KO description rather than KO id.
• str_width: str_width to wrap

Returns

ggplot

Examples

data("reporter_score_res")
plot_features_box(reporter_score_res,
  select_ko = c("K00059", "K00208", "K00647", "K00652", "K00833", "K01012"),
  box_param = list(p_value1 = FALSE, trend_line = TRUE)
)
plot_features_box(reporter_score_res,
  select_ko = "K00059", KO_description = TRUE,
  box_param = list(p_value1 = FALSE, trend_line = TRUE)
)