readImgData {SpatialExperiment} | R Documentation

## Read images & scale factors for 10x Genomics Visium

### Description

Function to read in images and scale factors for 10x Genomics Visium data, and return as a valid `imgData` `DataFrame`.

### Usage

    readImgData(
      path = ".",
      sample_id = names(path),
      imageSources = file.path(path, "tissue_lowres_image.png"),
      scaleFactors = file.path(path, "scalefactors_json.json"),
      load = TRUE
    )

### Arguments

`path` | a path where to find one or more images
`sample_id` | the `sample_id` for the `SpatialExperiment` object
`imageSources` | the images source path(s)
`scaleFactors` | the .json file where to find the scale factors
`load` | logical; should the image(s) be loaded into memory as a `grob`? If FALSE, will store the path/URL instead.

### Value

a `DataFrame`

### Author(s)

Helena L. Crowell

### Examples

    dir <- system.file(
      file.path("extdata", "10xVisium", "section1", "spatial"),
      package = "SpatialExperiment")

    # base directory contains
    # - scale factors (scalefactors_json.json)
    # - one image (tissue_lowres_image.png)
    list.files(dir)

    # read in images & scale factors
    # as valid 'imgData' 'DFrame'
    readImgData(dir, sample_id = "foo")

[Package SpatialExperiment version 1.4.0 Index]