Read Data From Vitessce

Source: R/preprocessing.R, R/convenience.R

Read in data from Vitessce-formatted JSON files

ReadVitessce(
  counts = NULL,
  coords = NULL,
  molecules = NULL,
  type = c("segmentations", "centroids"),
  filter = NA_character_
)

LoadHuBMAPCODEX(data.dir, fov, assay = "CODEX")

Arguments

counts

Path or URL to a Vitessce-formatted JSON file with expression data; should end in “.genes.json” or “.clusters.json”; pass NULL to skip

coords

Path or URL to a Vitessce-formatted JSON file with cell/spot spatial coordinates; should end in “.cells.json”; pass NULL to skip

molecules

Path or URL to a Vitessce-formatted JSON file with molecule spatial coordinates; should end in “.molecules.json”; pass NULL to skip

type

Type of cell/spot spatial coordinates to return, choose one or more from:

  • “segmentations” cell/spot segmentations

  • “centroids” cell/spot centroids

filter

A character to filter molecules by, pass NA to skip molecule filtering

data.dir

Path to a directory containing Vitessce cells and clusters JSONs

fov

Name to store FOV as

assay

Name to store expression matrix as

Value

ReadVitessce: A list with some combination of the following values:

  • “counts”: if counts is not NULL, an expression matrix with cells as columns and features as rows

  • “centroids”: if coords is not NULL and type is contains“centroids”, a data frame with cell centroids in three columns: “x”, “y”, and “cell”

  • “segmentations”: if coords is not NULL and type contains “centroids”, a data frame with cell segmentations in three columns: “x”, “y” and “cell”

  • “molecules”: if molecules is not NULL, a data frame with molecule spatial coordinates in three columns: “x”, “y”, and “gene”

LoadHuBMAPCODEX: A Seurat object

Note

This function requires the jsonlite package to be installed

Progress Updates with progressr

This function uses progressr to render status updates and progress bars. To enable progress updates, wrap the function call in with_progress or run handlers(global = TRUE) before running this function. For more details about progressr, please read vignette("progressr-intro")

Examples

if (FALSE) {
coords <- ReadVitessce(
  counts =
     "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.genes.json",
  coords =
     "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.cells.json",
  molecules =
     "https://s3.amazonaws.com/vitessce-data/0.0.31/master_release/wang/wang.molecules.json"
)
names(coords)
coords$counts[1:10, 1:10]
head(coords$centroids)
head(coords$segmentations)
head(coords$molecules)
}