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

knitr::opts_chunk$set(
  message = FALSE,
  dev = "ragg_png",
  fig.align = "center",
  pngquant = "--speed=10 --quality=30"
)

## -----------------------------------------------------------------------------
library(simona)
parents  = c("a", "a", "b", "b", "c", "d")
children = c("b", "c", "c", "d", "e", "f")
dag_small = create_ontology_DAG(parents, children)

## -----------------------------------------------------------------------------
dag_graphviz(dag_small)

## -----------------------------------------------------------------------------
color = 2:7
shape = c("polygon", "box", "oval", "egg", "diamond", "parallelogram")
dag_graphviz(dag_small, node_param = list(color = color, shape = shape))

## -----------------------------------------------------------------------------
color = c("a" = "red", "d" = "blue")
dag_graphviz(dag_small, node_param = list(color = color))

## -----------------------------------------------------------------------------
parents  = c("a", "a", "b", "b", "c", "d")
children = c("b", "c", "c", "d", "e", "f")
relations = c("is_a", "is_a", "part_of", "part_of", "is_a", "is_a")
dag_small = create_ontology_DAG(parents, children, relations = relations)

## -----------------------------------------------------------------------------
edge_color = c("is_a" = "red", "part_of" = "blue")
dag_graphviz(dag_small, edge_param = list(color = edge_color))

## -----------------------------------------------------------------------------
edge_color = c("a -> b" = "red", "c -> e" = "blue")
dag_graphviz(dag_small, edge_param = list(color = edge_color))

## ----comment = ''-------------------------------------------------------------
dag_as_DOT(dag_small, node_param = list(color = color, shape = shape)) |> cat()

## -----------------------------------------------------------------------------
dag = create_ontology_DAG_from_GO_db()
dag_graphviz(dag[, "GO:0010228"], 
    node_param = list(
        fillcolor = c("GO:0010228" = "pink"),
        style = c("GO:0010228" = "filled")
    ),
    edge_param = list(
        color = c("is_a" = "purple", "part_of" = "darkgreen"),
        style = c("is_a" = "solid", "part_of" = "dashed")
    ), width = 600, height = 600)

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

## ----fig.width = 9, fig.height = 7--------------------------------------------
dag_circular_viz(dag, partition_by_size = 5000)

## ----fig.width = 10, fig.height = 7-------------------------------------------
tree = dag_treelize(dag)
dag_circular_viz(tree)

## ----fig.width = 10, fig.height = 7-------------------------------------------
go_tb = readRDS(system.file("extdata", "sig_go_tb.rds", package = "simona"))
sig_go_ids = go_tb$ID[go_tb$p.adjust < 0.01]
# make sure `sig_go_ids` all in current GO.db version
sig_go_ids = intersect(sig_go_ids, dag_all_terms(dag))
dag_circular_viz(dag, highlight = sig_go_ids)

## -----------------------------------------------------------------------------
p.adjust = go_tb$p.adjust[go_tb$p.adjust < 0.01]

## -----------------------------------------------------------------------------
node_size_fun = function(x, range = c(2, 10)) {
    s = (range[2] - range[1])/(quantile(x, 0.95) - min(x)) * (x - min(x)) + range[1]
    s[s > range[2]] = range[2]
    s
}

## -----------------------------------------------------------------------------
library(ComplexHeatmap)
lgd = Legend(title = "p.adjust", at = -log10(c(0.01, 0.001, 0.0001)), 
    labels = c("0.01", "0.001", "0.0001"), type = "points",
    size = unit(node_size_fun(-log10(c(0.01, 0.001, 0.0001))), "pt"))

## -----------------------------------------------------------------------------
node_size = rep(2, dag_n_terms(dag))
names(node_size) = dag_all_terms(dag)
node_size[sig_go_ids] = node_size_fun(-log10(p.adjust))

## ----fig.width = 10, fig.height = 7-------------------------------------------
dag_circular_viz(dag, 
    highlight = sig_go_ids,
    node_size = node_size,
    edge_transparency = 0.92, 
    other_legends = lgd)

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