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Create a react app for digital unrolling

osddu.Rd

This function is used to start an interactive widget for digital unrolling. It requires a static files server to be hosted in order to find load the necessary files.

Usage

osddu(
  sampleID = 1,
  host = "127.0.0.1",
  port = "8080",
  width = NULL,
  height = NULL,
  elementId = NULL,
  quit = FALSE
)

Arguments

sampleID

A section ID

host

A host address

port

A valid port

width, height

Width and height of container

elementId

The element id of the widget

quit

A logical specifying is the app should quit

Value

A htmlwidget to be used in a shiny application

Examples


library(semla)
library(magick)

se_mcolon <- readRDS(system.file("extdata/mousecolon", 
                                 "se_mcolon", 
                                 package = "semla"))
# Load images
se_mcolon <- se_mcolon |> 
  LoadImages()
#> 
#> ── Loading H&E images ──
#> 
#> ℹ Loading image from /private/var/folders/8r/bfm2m_q17znfk0m_8dt330tm0000gp/T/RtmpLHpYU7/temp_libpath305b1609463d/semla/extdata/mousecolon/spatial/tissue_lowres_image.jpg
#> ℹ Scaled image from 541x600 to 400x444 pixels
#> ℹ Saving loaded H&E images as 'rasters' in Seurat object

# fetch path for one H&E image
im <- GetStaffli(se_mcolon)@imgs[1] |> 
  image_read()

# Get spatial network
spatnet <- GetSpatialNetwork(se_mcolon)[[1]]

if (FALSE) { # \dontrun{
# Tile image
tilepath <- TileImage(im = im, outpath = tempdir())

# Export spatial network as JSON
# Make sure that sampleID matches the ID of the H&E image
export_graph(se_mcolon, sampleID = 1, outdir = tilepath$datapath)

if (interactive()) {
# Host file server
file_server(hostDir = tilepath$datapath)

# Run widget
osddu(sampleID = 1,
      host = "127.0.0.1",
      port = 8080L,
      width = '800px',
      height = '800px',
      quit = FALSE)

beakr::stopAllServers()
}
} # }