Sample image visualization

Source: R/vis_image.R

This function visualizes the histology image for selected sample. Matches crop and settings of vis_clus() and vis_gene().

vis_image(
  spe,
  sampleid = unique(spe$sample_id)[1],
  image_id = "lowres",
  auto_crop = TRUE,
  is_stitched = FALSE,
  title_suffix = NULL
)

Arguments

spe

A SpatialExperiment-class object. See fetch_data() for how to download some example objects or read10xVisiumWrapper() to read in spaceranger --count output files and build your own spe object.

sampleid

A character(1) specifying which sample to plot from colData(spe)$sample_id (formerly colData(spe)$sample_name).

image_id

A character(1) with the name of the image ID you want to use in the background.

auto_crop

A logical(1) indicating whether to automatically crop the image / plotting area, which is useful if the Visium capture area is not centered on the image and if the image is not a square.

is_stitched

A logical(1) vector: If TRUE, expects a SpatialExperiment-class built with visiumStitched::build_spe(). http://research.libd.org/visiumStitched/reference/build_spe.html; in particular, expects a logical colData column exclude_overlapping specifying which spots to exclude from the plot. Sets auto_crop = FALSE.

title_suffix

A character(1) passed to paste() to modify the title of the plot following the sampleid.

Value

A ggplot2 object.

Details

This function subsets spe to the given sample and prepares the data and title for vis_clus_p().

See also

Other Spatial cluster visualization functions: frame_limits(), vis_clus(), vis_clus_p(), vis_grid_clus()

Examples


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

  ## Print the "lowres" image for sample 151673
  p1 <- vis_image(
    spe = spe,
    sampleid = "151673"
  )
  print(p1)

  ## Without auto-cropping the image
  p2 <- vis_image(
    spe = spe,
    sampleid = "151673",
    auto_crop = FALSE
  )
  print(p2)
}
#> 2025-04-30 17:48:50.873008 loading file /github/home/.cache/R/BiocFileCache/da1c215122_Human_DLPFC_Visium_processedData_sce_scran_spatialLIBD.Rdata%3Fdl%3D1