## ----echo = FALSE, message = FALSE--------------------------------------------
library(knitr)
knitr::opts_chunk$set(
    error = FALSE,
    tidy  = FALSE,
    message = FALSE,
    warning = FALSE,
    fig.align = "center")

## ----echo = FALSE-------------------------------------------------------------
knitr::knit_hooks$set(pngquant = knitr::hook_pngquant)

knitr::opts_chunk$set(
  dev = "ragg_png",
  fig.align = "center",
  pngquant = "--speed=10 --quality=50"
)

## -----------------------------------------------------------------------------
library(simona)
dag = create_ontology_DAG_from_GO_db(org_db = "org.Hs.eg.db")
dag

## -----------------------------------------------------------------------------
set.seed(888)
genes = random_items(dag, 500)
head(genes)

## -----------------------------------------------------------------------------
tb = dag_enrich_on_genes(dag, genes)
tb = tb[order(tb$p_adjust), ]
head(tb)

## -----------------------------------------------------------------------------
top_go_ids = tb$term[1:200]
mat = term_sim(dag, top_go_ids)

## ----fig.width = 6.5, fig.height = 6------------------------------------------
library(ComplexHeatmap)
Heatmap(mat, name = "similarity", 
    show_row_names = FALSE, show_column_names = FALSE,
    show_row_dend = FALSE, show_column_dend = FALSE)

## ----fig.width = 9, fig.height = 7--------------------------------------------
dag_circular_viz(dag, top_go_ids)

## ----fig.width = 8.5, fig.height = 4.34---------------------------------------
library(simplifyEnrichment)
simplifyEnrichment(mat)

## ----eval = FALSE-------------------------------------------------------------
#  library(AnnotationHub)
#  ah = AnnotationHub()
#  org_db = ah[["AH112417"]]
#  dag = create_ontology_DAG_from_GO_db(org_db = org_db)

## -----------------------------------------------------------------------------
dag = ontology_kw("human")
dag

## -----------------------------------------------------------------------------
genes = random_items(dag, 500)
tb = dag_enrich_on_genes(dag, genes)
tb = tb[order(tb$p_adjust), ]
top_go_ids = tb$term[1:50]

## ----fig.width = 6.5, fig.height = 6------------------------------------------
mat = term_sim(dag, top_go_ids)
Heatmap(mat, name = "similarity", 
    show_row_names = FALSE, show_column_names = FALSE,
    show_row_dend = FALSE, show_column_dend = FALSE)

## ----fig.width = 9, fig.height = 7--------------------------------------------
dag_circular_viz(dag, top_go_ids)

## ----fig.width = 5.5, fig.height = 4.34---------------------------------------
cl = simplifyEnrichment(mat)
head(cl)

## -----------------------------------------------------------------------------
dag = ontology_pw("human")
dag

## ----eval = FALSE-------------------------------------------------------------
#  # `genes` must be in symbols
#  tb = dag_enrich_on_genes(dag, genes)

## ----eval = FALSE-------------------------------------------------------------
#  dag = ontology_chebi("human")

## ----eval = FALSE-------------------------------------------------------------
#  # `genes` must be in symbols
#  tb = dag_enrich_on_genes(dag, genes)

## ----eval = FALSE-------------------------------------------------------------
#  dag = ontology_rdo("human")

## ----eval = FALSE-------------------------------------------------------------
#  # `genes` must be in symbols
#  tb = dag_enrich_on_genes(dag, genes)

## ----eval = FALSE-------------------------------------------------------------
#  dag = ontology_vt("human")

## ----eval = FALSE-------------------------------------------------------------
#  # `genes` must be in symbols
#  tb = dag_enrich_on_genes(dag, genes)

## -----------------------------------------------------------------------------
sessionInfo()