## ----setup, include = FALSE---------------------------------------------------
startTime <- Sys.time()
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    crop = NULL
)

library(dnaEPICO)

## ----overview-helpers, echo = FALSE, results = "asis"-------------------------
cat("
<style>
.overview-figure {
    margin: 1.5rem 0 2rem;
}

.overview-controls {
    display: flex;
    flex-wrap: wrap;
    gap: 8px;
    margin: 0 0 0.5rem;
}

.overview-zoom-button {
    background: #ffffff;
    border: 1px solid #2c7fb8;
    border-radius: 6px;
    color: #2c7fb8;
    cursor: pointer;
    font-size: 0.875rem;
    line-height: 1.2;
    padding: 5px 9px;
}

.overview-zoom-button:hover,
.overview-zoom-button:focus {
    background: #edf6fb;
}

.overview-zoom-value {
    align-items: center;
    color: #4b5563;
    display: inline-flex;
    font-size: 0.875rem;
    min-width: 44px;
}

.overview-svg-frame {
    background: #ffffff;
    border: 1px solid #d9e2ec;
    border-radius: 6px;
    max-height: 680px;
    overflow: auto;
    padding: 10px;
}

.overview-svg-frame img {
    display: block;
    height: auto;
    max-width: none;
    width: calc(1600px * var(--overview-scale, 1));
}

.overview-figure:fullscreen {
    background: #ffffff;
    margin: 0;
    overflow: hidden;
    padding: 16px;
}

.overview-figure:fullscreen .overview-svg-frame {
    height: calc(100vh - 88px);
    max-height: none;
}

@media (max-width: 768px) {
    .overview-svg-frame {
    max-height: 520px;
    }

    .overview-svg-frame img {
    width: calc(1200px * var(--overview-scale, 1));
    }
}
</style>
<script>
function setOverviewZoom(figureId, scale) {
    var figure = document.getElementById(figureId);
    if (!figure) {
    return;
    }

    var next = Math.max(0.5, Math.min(3, scale));
    figure.dataset.scale = next.toFixed(2);
    figure.style.setProperty('--overview-scale', next.toString());

    var label = figure.querySelector('.overview-zoom-value');
    if (label) {
    label.textContent = Math.round(next * 100) + '%';
    }
}

function changeOverviewZoom(figureId, delta) {
    var figure = document.getElementById(figureId);
    var current = figure ? parseFloat(figure.dataset.scale || '1') : 1;
    setOverviewZoom(figureId, current + delta);
}

function openOverviewFullscreen(figureId) {
    var figure = document.getElementById(figureId);
    if (!figure || !figure.requestFullscreen) {
    return;
    }

    figure.requestFullscreen();
}
</script>
")

overview_svgs <- c(
    preprocessingMinfiEwasWater =
        "preprocessingMinfiEwasWater_pipeline_overview.svg",
    svaEnmix =
        "svaEnmix_pipeline_overview.svg",
    preprocessingPheno =
        "preprocessingPheno_pipeline_overview.svg",
    methylationGLM =
        "methylationGLM_pipeline_overview.svg",
    methylationLME =
        "methylationLME_pipeline_overview.svg",
    dnamReport =
        "dnamReport_pipeline_overview.svg"
)

html_escape <- function(x) {
    x <- gsub("&", "&amp;", x, fixed = TRUE)
    x <- gsub("<", "&lt;", x, fixed = TRUE)
    x <- gsub(">", "&gt;", x, fixed = TRUE)
    x <- gsub('"', "&quot;", x, fixed = TRUE)
    x
}

svg_to_html <- function(svg_path, title = NULL) {
    if (!file.exists(svg_path)) {
        stop("Missing overview SVG: ", svg_path)
    }

    if (is.null(title)) {
        title <- sub(
            "_pipeline_overview$",
            "() overview",
            tools::file_path_sans_ext(basename(svg_path))
        )
    }

    figure_id <- gsub("[^A-Za-z0-9_-]", "-", tools::file_path_sans_ext(
        basename(svg_path)
    ))

    cat(sprintf(
        '<div class="overview-figure" id="%s" data-scale="1">\n',
        figure_id
    ))
    cat('<div class="overview-controls">\n')
    cat(sprintf(
        paste0(
            '<button class="overview-zoom-button" type="button" ',
            'onclick="changeOverviewZoom(\'%s\', 0.25)">',
            'Zoom +</button>\n'
        ),
        figure_id
    ))
    cat(sprintf(
        paste0(
            '<button class="overview-zoom-button" type="button" ',
            'onclick="changeOverviewZoom(\'%s\', -0.25)">',
            'Zoom -</button>\n'
        ),
        figure_id
    ))
    cat(sprintf(
        paste0(
            '<button class="overview-zoom-button" type="button" ',
            'onclick="setOverviewZoom(\'%s\', 1)">',
            'Reset</button>\n'
        ),
        figure_id
    ))
    cat(sprintf(
        paste0(
            '<button class="overview-zoom-button" type="button" ',
            'onclick="openOverviewFullscreen(\'%s\')">',
            'Full screen</button>\n'
        ),
        figure_id
    ))
    cat('<span class="overview-zoom-value">100%</span>\n')
    cat('</div>\n')
    cat('<div class="overview-svg-frame">\n')
    cat(sprintf(
        '<img src="%s" alt="%s">\n',
        html_escape(svg_path),
        html_escape(title)
    ))
    cat('\n</div>\n</div>\n')
}

## ----preprocessingMinfiEwasWater-overview, echo = FALSE, results = "asis"-----
svg_to_html(
    overview_svgs[["preprocessingMinfiEwasWater"]]
)

## ----svaEnmix-overview, echo = FALSE, results = "asis"------------------------
svg_to_html(
    overview_svgs[["svaEnmix"]])

## ----preprocessingPheno-overview, echo = FALSE, results = "asis"--------------
svg_to_html(
    overview_svgs[["preprocessingPheno"]])

## ----methylationGLM-overview, echo = FALSE, results = "asis"------------------
svg_to_html(
    overview_svgs[["methylationGLM"]])

## ----methylationLME-overview, echo = FALSE, results = "asis"------------------
svg_to_html(
    overview_svgs[["methylationLME"]])

## ----dnamReport-overview, echo = FALSE, results = "asis"----------------------
svg_to_html(
    overview_svgs[["dnamReport"]])

## ----vignette-date, echo = FALSE----------------------------------------------
Sys.time()

## ----vignette-wallclock, echo = FALSE-----------------------------------------
totalTime <- diff(c(startTime, Sys.time()))
round(totalTime, digits = 3)

## ----vignette-session-info, echo = FALSE--------------------------------------
sessionInfo()