## ----vignette-setup, include=FALSE--------------------------------------------
fig_path <-
    if (knitr::opts_knit$get("child")) {
        "../../man/figures/"
    } else {
        "../man/figures/"
    }

knitr::opts_chunk$set(
    cache = TRUE,
    echo = TRUE,
    fig.path = fig_path
)

## ----load_packages, include=TRUE, results="hide", message=FALSE, warning=FALSE----
library(imageFeatureTCGA)
library(HistoImagePlot)
library(dplyr)
library(SpatialExperiment)
library(ggplot2)

## ----install, eval=FALSE------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly = TRUE))
#     install.packages("BiocManager")
# 
# BiocManager::install("waldronlab/HistoImagePlot")

## ----h5ad---------------------------------------------------------------------
hov_file <- paste0(
    "https://store.cancerdatasci.org/hovernet/h5ad/",
    "TCGA-23-1021-01Z-00-DX1.F07C221B-D401-47A5-9519-10DE59CA1E9D.h5ad.gz")

thumb_path <- paste0(
    "https://store.cancerdatasci.org/hovernet/thumb/",
    "TCGA-23-1021-01Z-00-DX1.F07C221B-D401-47A5-9519-10DE59CA1E9D.png")

hn_spe <- HoverNet(hov_file, outClass = "SpatialExperiment") |>
    import()

## ----overlay-basic, fig.width=12, fig.height=6--------------------------------

thumb_path <- paste0(
    "https://store.cancerdatasci.org/hovernet/thumb/",
    "TCGA-23-1021-01Z-00-DX1.F07C221B-D401-47A5-9519-10DE59CA1E9D.png")

plotHoverNetH5ADOverlay(hn_spe, thumb_path)

## ----overlay-custom, fig.width=12, fig.height=6-------------------------------
plotHoverNetH5ADOverlay(
    hn_spe,
    thumb_path,
    title = "Ovarian Cancer Tissue - Cell Segmentation",
    point_size = 0.02,
    legend_point_size = 3
)

## ----overlay-colors, fig.width=12, fig.height=6-------------------------------
custom_colors <- c(
    "no label" = "#808080",
    "neoplastic" = "#E31A1C",
    "inflammatory" = "#1F78B4",
    "stromal" = "#33A02C",
    "necrotic" = "#FF7F00",
    "benign epithelial" = "#6A3D9A"
)

plotHoverNetH5ADOverlay(
    hn_spe,
    thumb_path,
    color_palette = custom_colors,
    title = "Custom Color Scheme"
)

## ----h5ad-features, fig.width=10, fig.height=8--------------------------------
h5ad_coords <- data.frame(spatialCoords(hn_spe), colData(hn_spe))

p1 <- ggplot(h5ad_coords, aes(x = x_centroid, y = y_centroid, 
                            color = mean_intensity)) +
    geom_point(size = 0.5) +
    scale_color_viridis_c() +
    coord_fixed() +
    theme_minimal() +
    labs(title = "Mean Intensity", color = "Intensity")

p2 <- ggplot(h5ad_coords, aes(x = x_centroid, y = y_centroid, 
                                color = nearest_neighbor_distance)) +
    geom_point(size = 0.5) +
    scale_color_viridis_c(option = "plasma") +
    coord_fixed() +
    theme_minimal() +
    labs(title = "Nearest Neighbor Distance", color = "Distance")

cowplot::plot_grid(p1, p2, ncol = 2)

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

