rich_forest: Barplot for GSEA results

In Yutong441/TBdev: Infer a Trophoblast Developmental Trajectory

Description

This function creates a compact way of visualising GSEA results by creating multiple tree-like plots, or 'forests' (silva in Latin). Each tree represents a pairwise comparison between one particular cell type with all other cell types. This pattern is repeated for other cell types as well. Each cell pair comparison is marked by an arrow (sagitta in Latin) on top

Usage

rich_forest(
  plot_data,
  markers,
  organism_db,
  show_num = 4,
  show_gene_labels = 3,
  category_col = "category",
  pval_col = "p.adjust",
  enrich_col = "value",
  term_col = "termID",
  group1 = "cluster",
  group2 = "compare_group",
  simplification = T,
  sim_dict = NULL,
  append_default_dict = T,
  compare_group_col_marker = "compare_group",
  AP = NULL,
  ...
)

Arguments

plot_data	a dataframe generated from run_GSEA_all_types. NB: if the input data frame is from other functions, make sure you apply some p value cut off. It must have the following columns:
markers	a dataframe generated from find_DE_genes that contain the log fold change of gene expression. This information is used to order the appearance of genes in the plot labels. It must contain the columns: group (group1), logFC (used to rate which genes to show), feature (genes), and compare_group (group2). You can change compare_group via:
organism_db	a gene database
show_num	how many terms to show per pairwise comparison
show_gene_labels	how many genes to show after each term
category_col	the GSEA terms
pval_col	the (adjusted) p value
enrich_col	the enrichment value
term_col	the ID for each gene in the format of A.B.entrez where A and B can be of anything and entrez means entrez ID
group1	comparison group1. Each group in cluster will be in a
group2	comparison group2. Each group here will be in the same tree.
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 not exist.
compare_group_col_marker	which column in markers contain the group2 information.
AP	aesthetic parameters for plotting
...	other parameters to pass onto gg_silva and sagittae.
separate	tree. You may change it by specifying group=...'

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