ReadVizgen: Read and Load MERFISH Input from Vizgen

In Seurat: Tools for Single Cell Genomics

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")

Note

This function requires the data.table package to be installed

Seurat documentation built on Nov. 18, 2023, 1:10 a.m.