plotContour.R

#' Plot contour lines.
#'
#' @param spe A SpatialExperiment object.
#' @param coi A character vector of length 1 of the cell type of interest.
#' @param overlay Character vector. Either plot overlay on density or cell.
#' By default is cell.
#' @param id A character. The name of the column of colData(spe) containing
#' the cell type identifiers. Set to cell_type by default.
#' @param sub.level Character vector. Subset on specific level.
#' @param ... Aesthetic mappings to pass to `ggplot2::aes_string()`.
#'
#' @return A ggplot object.
#' @export
#'
#' @examples
#'
#' data("xenium_bc_spe")
#'
#' spe <- gridDensity(spe)
#'
#' coi <- "Breast cancer"
#'
#' spe <- getContour(spe, coi = coi)
#'
#' plotContour(spe, coi = coi, size = 0.3, alpha = 0.2)
#'
plotContour <- function(spe,
                        coi,
                        overlay = c("cell", "density"),
                        id = "cell_type",
                        sub.level = NULL, ...) {
    if (length(coi) > 1L) {
        stop("coi must be of length 1!")
    }

    if (!(coi %in% colData(spe)[[id]])) {
        stop("coi not in colData(spe)[[id]]!")
    }

    coi_clean <- janitor::make_clean_names(coi)
    coi_clean_contour <- paste(coi_clean, "contour", sep = "_")

    if (!coi_clean_contour %in% names(spe@metadata)) {
        stop("Contour of coi doesn't exist. Please run getContour() first!")
    }

    contour_data <- as.data.frame(spe@metadata[[coi_clean_contour]])
    levs <- unique(contour_data$level)
    nlevs <- length(levs)

    if (length(overlay) == 2) {
        overlay <- "cell"
    }

    if (overlay == "cell") {
        sub <- grep(coi, colData(spe)[[id]])
        p <- plotSpatial(spe[, sub], ...)
    } else if (overlay == "density") {
        p <- plotDensity(spe, coi = coi, ...)
    } else {
        stop("Overlay should either be cell or density.")
    }

    col.p <- grDevices::colorRampPalette(col.spec)(
        length(unique(contour_data$level)))

    if (is.null(sub.level)) {
        suppressMessages(p <- p +
            ggplot2::geom_path(
                data = contour_data,
                ggplot2::aes(
                    x = x, y = y, group = group,
                    color = level
                )
            ) +
            scale_color_manual(name = "Density level", values = rev(col.p)))
    } else {
        if (length(sub.level) == 1L & sub.level %in% contour_data$level) {
            suppressMessages(p <- p +
                ggplot2::geom_path(
                    data = contour_data,
                    ggplot2::aes(
                        x = x, y = y, group = group,
                        color = level == sub.level
                    )
                ) +
                scale_color_manual(
                    name = paste0("level", sub.level, " density"),
                    values = c("royalblue", "tomato2")
                ))
        } else {
            stop("The length sub.level is expected to be 1 and
           should be included in contour_data$level.")
        }
    }

    p <- p +
        theme_classic() +
        labs(x = "x", y = "y") +
        ggtitle(coi)
    return(p)
}


utils::globalVariables(c("x", "y", "group", "level"))