read_steinbock {imcRtools} | R Documentation

## Reads in single-cell data generated by the steinbock pipeline

### Description

Reader function to generate a `SpatialExperiment` or `SingleCellExperiment` object from single-cell data obtained by the steinbock pipeline.

### Usage

    read_steinbock(
      path,
      intensities_folder = "intensities",
      regionprops_folder = "regionprops",
      graphs_folder = "neighbors",
      pattern = NULL,
      extract_cellid_from = "Object",
      extract_coords_from = c("centroid-1", "centroid-0"),
      image_file = "images.csv",
      extract_imagemetadata_from = c("width_px", "height_px"),
      panel_file = "panel.csv",
      extract_names_from = "name",
      return_as = c("spe", "sce"),
      BPPARAM = SerialParam()
    )

### Arguments

`path` | full path to the steinbock output folder
`intensities_folder` | name of the folder containing the intensity measurements per image
`regionprops_folder` | name of the folder containing the cell-specific morphology and spatial measurements per image. Can be set to `NULL` to exclude reading in morphology measures.
`graphs_folder` | name of the folder containing the spatial connectivity graphs per image. Can be set to `NULL` to exclude reading in graphs.
`pattern` | regular expression specifying a subset of files that should be read in.
`extract_cellid_from` | single character indicating which column entry in the intensity files contains the integer cell id.
`extract_coords_from` | character vector indicating which column entries in the regionprops files contain the x (first entry) and y (second entry) coordinates.
`image_file` | single character indicating the file name storing meta data per image (can be `NULL`).
`extract_imagemetadata_from` | character vector indicating which additional image specific metadata to extract from the `image_file`. These will be stored in the `colData(x)` slot as object/cell-specific entries.
`panel_file` | single character containing the name of the panel file. This can either be inside the steinbock path (recommended) or located somewhere else.
`extract_names_from` | single character indicating the column of the panel file containing the channel names.
`return_as` | should the object be returned as `SpatialExperiment` (`return_as = "spe"`) or `SingleCellExperiment` (`return_as = "sce"`).
`BPPARAM` | parameters for parallelised processing.

### Value

returns a `SpatialExperiment` or `SingleCellExperiment` object markers in rows and cells in columns.

### The returned data container

In the case of both containers `x`, intensity features are stored in the `counts(x)` slot. Morphological features are stored in the `colData(x)` slot. The graphs are stored as `SelfHits` object in the `colPair(x, "neighborhood")` slot.

In the case of a returned `SpatialExperiment` object, the cell coordinates are stored in the `spatialCoords(x)` slot.

In the case of a returned `SingleCellExperiment` object, the cell coordinates are stored in the `colData(x)` slot named as `Pos_X` and `Pos_Y`.

### Author(s)

Nils Eling (nils.eling@dqbm.uzh.ch)

### See Also

https://github.com/BodenmillerGroup/steinbock for the pipeline

`read_cpout` for reading in single-cell data as produced by the ImcSegmentationPipeline

`SingleCellExperiment` and `SpatialExperiment` for the constructor functions.

`colPair` for information on how to work with the cell-cell interaction graphs

`bpparam` for the parallelised backend

### Examples

    path <- system.file("extdata/mockData/steinbock", package = "imcRtools")

    # Read in as SpatialExperiment object
    x <- read_steinbock(path)
    x

    # Read in as SingleCellExperiment object
    x <- read_steinbock(path, return_as = "sce")
    x

    # Read in a subset of files
    x <- read_steinbock(path, pattern = "mockData1")
    x

    # Only read in intensities
    x <- read_steinbock(path, graphs_folder = NULL, regionprops_folder = NULL)
    x

    # Parallelisation
    x <- read_steinbock(path, BPPARAM = BiocParallel::bpparam())

[Package imcRtools version 1.0.2 Index]