## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, comment = "#>")

## ----setup--------------------------------------------------------------------
library(BioTooltipR)
use_bio_tooltips(
  modules = c("gene", "chemical")
)

## ----inline-demo, results='asis'----------------------------------------------
cat("The tumour suppressor ", gene_tt("TP53", species = "human"), " is central to DNA damage responses.", sep = "")

## ----chemical-demo, results='asis'--------------------------------------------
cat("A chemical example: ", chem_tt("aspirin", query = "2244", scope = "pubchem"), ".", sep = "")

## ----table-demo, results='asis'-----------------------------------------------
top_genes <- data.frame(
  symbol = c("TP53", "BRCA1", "GADD45A"),
  log2FoldChange = c(2.1, -1.4, 1.2),
  padj = c(0.0004, 0.002, 0.01)
)

top_genes |>
  gene_column(symbol, species = "human") |>
  bt_kable(include_setup = FALSE)

## ----cdn-demo, eval=FALSE-----------------------------------------------------
# use_bio_tooltips(cdn = TRUE, version = "2.0.9")

## ----volcano-demo, message=FALSE, warning=FALSE-------------------------------
if (!requireNamespace("plotly", quietly = TRUE) ||
    !requireNamespace("htmlwidgets", quietly = TRUE)) {
  htmltools::tags$p(
    "Install the optional plotly and htmlwidgets packages to render this interactive example."
  )
} else {
set.seed(42)

volcano_genes <- c(
  "TP53", "BRCA1", "BRCA2", "EGFR", "MYC", "PTEN", "KRAS", "NRAS",
  "BRAF", "CDK1", "CCND1", "CDKN1A", "CDKN2A", "MDM2", "RB1", "ATM",
  "ATR", "CHEK1", "CHEK2", "GADD45A", "VEGFA", "HIF1A", "IL6", "TNF",
  "CXCL8", "STAT3", "JAK2", "AKT1", "MTOR", "PIK3CA", "FOXO3", "ESR1",
  "AR", "ERBB2", "MET", "ALK", "ROS1", "NTRK1", "RET", "APC",
  "CTNNB1", "SMAD4", "TGFB1", "MMP2", "MMP9", "COL1A1", "COL3A1",
  "FN1", "VIM", "CDH1", "EPCAM", "SOX2", "NANOG", "POU5F1", "MKI67",
  "AURKA", "TOP2A", "BCL2", "BAX"
)

set.seed(42)

n <- length(volcano_genes)

# Most genes are unchanged; a minority have a real effect.
is_de <- rbinom(n, size = 1, prob = 0.18)

true_lfc <- ifelse(
  is_de == 1,
  sample(c(-1, 1), n, replace = TRUE) *
    pmax(0.5, rnorm(n, mean = 1.25, sd = 0.45)),
  0
)

# Different genes have different measurement precision.
# This is important: it prevents significance from being a simple
# deterministic function of fold change.
se <- exp(rnorm(n, mean = log(0.38), sd = 0.35))

# Observed fold change.
log2FoldChange <- true_lfc + rnorm(n, mean = 0, sd = se)

volcano <- data.frame(
  symbol = volcano_genes,
  log2FoldChange = log2FoldChange,
  se = se
)

# Keep a few visually interesting, recognizable genes.
interesting <- data.frame(
  symbol = c(
    "MYC", "EGFR", "VEGFA", "IL6", "MMP9", "MKI67",
    "TP53", "BRCA1", "CDKN1A", "PTEN", "CDH1", "BAX"
  ),
  log2FoldChange = c(
     2.6,  1.9,  1.7,  2.2,  1.5,  2.9,
    -2.1, -1.8, -1.4, -1.7, -2.4, -1.3
  ),
  se = c(
    0.46, 0.45, 0.52, 0.48, 0.52, 0.50,
    0.46, 0.48, 0.46, 0.50, 0.45, 0.48
  )
)

idx <- match(interesting$symbol, volcano$symbol)

volcano$log2FoldChange[idx] <- interesting$log2FoldChange
volcano$se[idx] <- interesting$se

# Wald-like significance test.
volcano$statistic <- volcano$log2FoldChange / volcano$se
volcano$pvalue <- 2 * pnorm(-abs(volcano$statistic))
volcano$padj <- p.adjust(volcano$pvalue, method = "BH")

volcano$neg_log10_padj <- -log10(volcano$padj)
volcano$direction <- ifelse(
  volcano$padj < 0.05 & volcano$log2FoldChange >= 1,
  "Up-regulated",
  ifelse(
    volcano$padj < 0.05 & volcano$log2FoldChange <= -1,
    "Down-regulated",
    "Not significant"
  )
)
volcano$direction <- factor(
  volcano$direction,
  levels = c("Up-regulated", "Down-regulated", "Not significant")
)
volcano$label <- ifelse(volcano$symbol %in% interesting$symbol, volcano$symbol, "")

volcano_plot <- plotly::plot_ly(
  volcano,
  x = ~log2FoldChange,
  y = ~neg_log10_padj,
  key = ~symbol,
  type = "scatter",
  mode = "markers+text",
  text = ~label,
  textposition = "top center",
  color = ~direction,
  colors = c(
    "Up-regulated" = "#b91c1c",
    "Down-regulated" = "#2563eb",
    "Not significant" = "#7a7f87"
  ),
  marker = list(size = 9, opacity = 0.82, line = list(width = 0)),
  textfont = list(size = 10, color = "#24292f")
) |>
  plotly::layout(
    xaxis = list(title = "log2 fold change", zeroline = TRUE),
    yaxis = list(title = "-log10 adjusted p-value"),
    legend = list(orientation = "h", x = 0, y = 1.12),
    margin = list(t = 60),
    shapes = list(
      list(type = "line", x0 = -1, x1 = -1, y0 = 0, y1 = 4.6,
           line = list(color = "#b7bdc5", width = 1, dash = "dot")),
      list(type = "line", x0 = 1, x1 = 1, y0 = 0, y1 = 4.6,
           line = list(color = "#b7bdc5", width = 1, dash = "dot")),
      list(type = "line", x0 = -3.2, x1 = 3.2, y0 = -log10(0.05), y1 = -log10(0.05),
           line = list(color = "#b7bdc5", width = 1, dash = "dot"))
    )
  )

bt_plotly_gene_hover(volcano_plot, species = "human", include_setup = FALSE)
}

## ----auto-demo----------------------------------------------------------------
auto_gene_tooltips(
  genes = c("Trp53", "Brca1", "Gadd45a"),
  species = "mouse",
  selector = ".auto-link-demo",
  include_setup = FALSE
)