VisiumExperiment-class {SpatialExperiment} | R Documentation

## The VisiumExperiment class

### Description

The VisiumExperiment class is designed to represent 10x Visium spatial Gene Expression data. It inherits from the SpatialExperiment class and is used in the same manner. In addition, the class supports the integration with 10x Visium spatial coordinates and its scale factors.

### Usage

    VisiumExperiment(..., scaleFactors = list(), imagePaths = list())

### Arguments

`...` | arguments to be passed to the `SpatialExperiment` constructor to fill the slots of the base class.
`scaleFactors` | the 10x Visium image scale factors.
`imagePaths` | the list of the paths for the 10x Visium images.

### Value

none

### Slots

`scaleFactors`

  list

`imagePaths`

  list

### Author(s)

Dario Righelli

### Examples

    barcodesFile <- system.file(file.path("extdata", "10x_visium",
                            "barcodes.tsv"),
                            package="SpatialExperiment")
    barcodesEx <- read.csv(barcodesFile, sep="\t",
                            header=FALSE, col.names=c("Barcodes"))
    featuresFile <- system.file(file.path("extdata", "10x_visium",
                            "features.tsv"), package="SpatialExperiment")
    featuresEx <- read.csv(featuresFile, sep="\t",
                            header=FALSE, col.names=c("Barcodes", "Feature_name",
                            "Feature_type"))
    countsFile <- system.file(file.path("extdata", "10x_visium",
                            "matrix.mtx"), package="SpatialExperiment")
    countsEx <- Matrix::readMM(file=countsFile)
    posFile <- system.file(file.path("extdata", "10x_visium",
                            "tissue_positions_list.tsv"),
                            package="SpatialExperiment")
    tissPosEx <- read.csv(posFile,
                            sep="\t", header=FALSE,
                            col.names=c("Barcodes", "in_tissue",
                             "array_row", "array_col",
                             "pxl_col_in_fullres", "pxl_row_in_fullres"))
    scaleFile <- system.file(file.path("extdata", "10x_visium",
                                       "scalefactors_json.json"),
                             package="SpatialExperiment")

    scalefactors <- rjson::fromJSON(file=scaleFile)
    imagePaths <- list.files(system.file(file.path("extdata", "10x_visium",
                             "images"),
                             package="SpatialExperiment"), full.names=TRUE)

    ve <- VisiumExperiment(rowData=featuresEx, colData=barcodesEx,
                             assays=c(counts=countsEx),
                             spatialCoords=tissPosEx,
                             scaleFactors=scalefactors,
                             imagePaths=imagePaths)

    ve

[Package SpatialExperiment version 1.0.0 Index]