A ggplot2 layer for visualizing the Visium histology

This function defines a ggplot2::layer() for visualizing the histology image from Visium. It can be combined with other ggplot2 functions for visualizing the clusters as in vis_clus_p() or gene-level information as in vis_gene_p().

geom_spatial(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  ...
)

Arguments

mapping: Passed to ggplot2::layer(mapping) where grob, x and y are required.
data: Passed to ggplot2::layer(data).
stat: Passed to ggplot2::layer(stat).
position: Passed to ggplot2::layer(position).
na.rm: Passed to ggplot2::layer(params = list(na.rm)).
show.legend: Passed to ggplot2::layer(show.legend).
inherit.aes: Passed to ggplot2::layer(inherit.aes).
...: Other arguments passed to ggplot2::layer(params = list(...)).

Value

A ggplot2::layer() for the histology information.

Author

10x Genomics

Examples


if (enough_ram()) {
    ## Obtain the necessary data
    if (!exists("spe")) spe <- fetch_data("spe")

    ## Select the first sample and extract the data
    sample_id <- unique(spe$sample_id)[1]
    spe_sub <- spe[, spe$sample_id == sample_id]
    sample_df <- as.data.frame(colData(spe_sub), optional = TRUE)

    ## Obtain the histology image
    img <- SpatialExperiment::imgRaster(spe_sub)

    ## Transform to a rasterGrob object
    grob <- grid::rasterGrob(img, width = grid::unit(1, "npc"), height = grid::unit(1, "npc"))

    ## Make a plot using geom_spatial
    p <- ggplot2::ggplot(
        sample_df,
        ggplot2::aes(
            x = pxl_col_in_fullres * SpatialExperiment::scaleFactors(spe_sub),
            y = pxl_row_in_fullres * SpatialExperiment::scaleFactors(spe_sub),
        )
    ) +
        geom_spatial(
            data = tibble::tibble(grob = list(grob)),
            ggplot2::aes(grob = grob),
            x = 0.5,
            y = 0.5
        )

    ## Show the plot
    print(p)

    ## Clean up
    rm(spe_sub)
}
#> 2024-10-31 20:26:24.415304 loading file /github/home/.cache/R/BiocFileCache/f6f1918e278_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1