---
title: "Heatmaps"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Heatmaps}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

```{r setup}
library(ggcolonviz)
library(ggplot2)
```

## Heatmaps

You can create heatmaps to visualize the severity of inflammation across different parts of the colon.

```{r heatmap}
# Assign a continuous score based on anatomy
# Example: Gradient that follows the 'y' axis for vertical parts
heatmap_points <- colon_heatmap_grid() |>
  dplyr::mutate(
    severity = dplyr::case_when(
      part == "Transverse" ~ (x + 3.5) / 4, # Heat flows left-to-right
      TRUE ~ (y + 1) / 6 # Heat flows bottom-to-top
    )
  )

# Sample lesion data (Coordinates must match your blueprint's dx/dy space)
lesions <- data.frame(
  x = c(-3.0, 0.0, -0.2), # Specific anatomical locations
  y = c(2.0, 4.3, 0.5),
  type = c("Polyp", "Ulcer", "Polyp"),
  size = c(4, 2, 6)
)

ggplot() +
  # Layer 1: Internal Heatmap
  geom_raster(data = heatmap_points, aes(x = x, y = y, fill = severity)) +

  # Layer 2: Discrete Lesions
  geom_point(
    data = lesions,
    aes(x = x, y = y, shape = type, size = size),
    color = "cyan",
    fill = "black",
    stroke = 1.2
  ) +

  # Styling
  scale_fill_viridis_c(option = "magma", name = "Tissue Heat") +
  scale_size_continuous(range = c(2, 6), guide = "none") +
  coord_fixed(expand = FALSE) +
  theme_void() +
  labs(title = "Subject 001: Integrated Colonic Heatmap & Lesion Map")
```