ReadVizgen: Read and Load MERFISH Input from Vizgen
In satijalab/seurat: Tools for Single Cell Genomics

ReadVizgen

R Documentation

Read and Load MERFISH Input from Vizgen

Description

Read and load in MERFISH data from Vizgen-formatted files

Usage

ReadVizgen(
  data.dir,
  transcripts = NULL,
  spatial = NULL,
  molecules = NULL,
  type = "segmentations",
  mol.type = "microns",
  metadata = NULL,
  filter = NA_character_,
  z = 3L
)

LoadVizgen(data.dir, fov, assay = "Vizgen", z = 3L)

Arguments

`data.dir`	Path to the directory with Vizgen MERFISH files; requires at least one of the following files present: “`cell_by_gene.csv`”: used for reading count matrix “`cell_metadata.csv`”: used for reading cell spatial coordinate matrices “`detected_transcripts.csv`”: used for reading molecule spatial coordinate matrices
`transcripts`	Optional file path for counts matrix; pass `NA` to suppress reading counts matrix
`spatial`	Optional file path for spatial metadata; pass `NA` to suppress reading spatial coordinates. If `spatial` is provided and `type` is “segmentations”, uses `dirname(spatial)` instead of `data.dir` to find HDF5 files
`molecules`	Optional file path for molecule coordinates file; pass `NA` to suppress reading spatial molecule information
`type`	Type of cell spatial coordinate matrices to read; choose one or more of: “segmentations”: cell segmentation vertices; requires hdf5r to be installed and requires a directory “`cell_boundaries`” within `data.dir`. Within “`cell_boundaries`”, there must be one or more HDF5 file named “`feature_data_##.hdf5`” “centroids”: cell centroids in micron coordinate space “boxes”: cell box outlines in micron coordinate space
`mol.type`	Type of molecule spatial coordinate matrices to read; choose one or more of: “pixels”: molecule coordinates in pixel space “microns”: molecule coordinates in micron space
`metadata`	Type of available metadata to read; choose zero or more of: “volume”: estimated cell volume “fov”: cell's fov
`filter`	A character to filter molecules by, pass `NA` to skip molecule filtering
`z`	Z-index to load; must be between 0 and 6, inclusive
`fov`	Name to store FOV as
`assay`	Name to store expression matrix as

Value

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

“transcripts”: a sparse matrix with expression data; cells are columns and features are rows
“segmentations”: a data frame with cell polygon outlines in three columns: “x”, “y”, and “cell”
“centroids”: a data frame with cell centroid coordinates in three columns: “x”, “y”, and “cell”
“boxes”: a data frame with cell box outlines in three columns: “x”, “y”, and “cell”
“microns”: a data frame with molecule micron coordinates in three columns: “x”, “y”, and “gene”
“pixels”: a data frame with molecule pixel coordinates in three columns: “x”, “y”, and “gene”
“metadata”: a data frame with the cell-level metadata requested by metadata

LoadVizgen: A Seurat object

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")

Parallelization with future

This function uses future to enable parallelization. Parallelization strategies can be set using plan. Common plans include “sequential” for non-parallelized processing or “multisession” for parallel evaluation using multiple R sessions; for other plans, see the “Implemented evaluation strategies” section of ?future::plan. For a more thorough introduction to future, see vignette("future-1-overview")