## ----setup, include=FALSE-----------------------------------------------------
knitr::opts_chunk$set(cache = TRUE, echo = TRUE)

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

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

## ----getcatalog---------------------------------------------------------------
getCatalog()

## ----listhover----------------------------------------------------------------
getCatalog("hovernet")

## ----listprovgiga-------------------------------------------------------------
getCatalog("provgigapath")

## ----importHover--------------------------------------------------------------
hspe <- getCatalog("hovernet") |>
    dplyr::filter(
        filename == paste(
            "TCGA-VG-A8LO-01A-01-DX1",
            "B39A4D64-82A1-4A04-8AB6-918F3058B83B",
            "json",
            "gz",
            sep = "."
        )
    ) |>
    getFileURLs() |>
    HoverNet(outClass = "SpatialExperiment") |>
    import()
hspe

## ----spcoords-----------------------------------------------------------------
colData(hspe)

## ----importProvGiga-----------------------------------------------------------
getCatalog("provgigapath") |>
    dplyr::filter(
        filename == paste(
            "TCGA-VG-A8LO-01A-01-DX1",
            "B39A4D64-82A1-4A04-8AB6-918F3058B83B",
            "csv",
            "gz",
            sep = "."
        ) &
        level == "slide_level"
    ) |>
    getFileURLs() |>
    ProvGiga() |>
    import()

## -----------------------------------------------------------------------------
getCatalog("provgigapath") |>
    dplyr::filter(
        filename == paste(
            "TCGA-VG-A8LO-01A-01-DX1",
            "B39A4D64-82A1-4A04-8AB6-918F3058B83B",
            "csv",
            "gz",
            sep = "."
        ) &
        level == "tile_level"
    ) |>
    getFileURLs() |>
    ProvGiga() |>
    import()

## ----ProvGigaList-------------------------------------------------------------
pgl <- getCatalog("provgigapath") |>
    dplyr::filter(level == "slide_level", Project.ID == "TCGA-GBM") |>
    dplyr::slice(1:3) |>
    getFileURLs() |>
    ProvGigaList() |>
    import()
pgl

## ----ProvGigaListMixed--------------------------------------------------------
pgl_mixed <- getCatalog("provgigapath") |>
    dplyr::filter(
        filename %in% c(
            paste(
                "TCGA-VG-A8LO-01A-01-DX1",
                "B39A4D64-82A1-4A04-8AB6-918F3058B83B",
                "csv",
                "gz",
                sep = "."
            )
        ) &
        level %in% c("slide_level", "tile_level")
    ) |>
    getFileURLs() |>
    ProvGigaList() |>
    import()
pgl_mixed

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