plot_features_in_pathway function

Plot features trend in one pathway or module

plot_features_in_pathway(
  ko_stat,
  map_id = "map00780",
  modulelist = NULL,
  select_ko = NULL,
  box_color = reporter_color,
  show_number = TRUE,
  scale = FALSE,
  feature_type = "KOs",
  line_color = c(Depleted = "seagreen", Enriched = "orange", None = "grey", Significant =
    "red2")
)

Arguments

• ko_stat: ko_stat result from pvalue2zs or result of get_reporter_score
• map_id: the pathway or module id
• modulelist: NULL or customized modulelist dataframe, must contain "id","K_num","KOs","Description" columns. Take the KOlist as example, use custom_modulelist.
• select_ko: select which ko
• box_color: box and point color, default: c("#e31a1c","#1f78b4")
• show_number: show the numbers.
• scale: scale the data by row.
• feature_type: show in the title ,default: KOs
• line_color: line color, default: c("Depleted"="seagreen","Enriched"="orange","None"="grey")

Returns

ggplot

Examples

data("reporter_score_res")
plot_features_in_pathway(ko_stat = reporter_score_res, map_id = "map00860")