display_cluster_enrichment: Visualise results from over-representation test

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

need to set seed to ensure reproducibility

Usage

display_cluster_enrichment(
  xx,
  show_graph = "emap",
  feature_vec = NULL,
  default_theme = F,
  save_dir = NULL,
  enrich_area = "GO",
  show_num = NULL,
  clean_results = T,
  simplification = T,
  AP = NULL,
  sim_dict = NULL,
  append_default_dict = T,
  subset_cluster = NULL,
  organism_db = NULL,
  num_col = NULL,
  markers = NULL,
  ...
)

Arguments

xx	result from compareCluster or just a dataframe
show_graph	whether to show the terms in piechart format ('emap') or dotplot ('dotplot') or ridgeplot ('ridgeplot')
feature_vec	to manually assign color
default_theme	whether to use ggplot default theme
enrich_area	either 'GO', 'KEGG' or 'reactome'. Only important for saving the figure
clean_results	whether to remove unrelated and disease related terms
simplification	whether to simplify the GO/KEGG/reactome terms
sim_dict	a data frame with 2 columns: 'ori' for the original terms, 'sub' for the strings that will replace the original terms. The default is a a limited data frame built into this package.
append_default_dict	append default dictionary to simplify the terms

Yutong441/TBdev documentation built on Dec. 18, 2021, 8:22 p.m.