Read and Load Nanostring SMI data
ReadNanostring(
data.dir,
mtx.file = NULL,
metadata.file = NULL,
molecules.file = NULL,
segmentations.file = NULL,
type = "centroids",
mol.type = "pixels",
metadata = NULL,
mols.filter = NA_character_,
genes.filter = NA_character_,
fov.filter = NULL,
subset.counts.matrix = NULL,
cell.mols.only = TRUE
)LoadNanostring(data.dir, fov, assay = "Nanostring")
ReadNanostring
: A list with some combination of the
following values:
“matrix
”: a
sparse matrix with expression data; cells
are columns and features are rows
“centroids
”: a data frame with cell centroid
coordinates in three columns: “x”, “y”, and “cell”
“pixels
”: a data frame with molecule pixel coordinates
in three columns: “x”, “y”, and “gene”
LoadNanostring
: A Seurat
object
Path to folder containing Nanostring SMI outputs
Path to Nanostring cell x gene matrix CSV
Contains metadata including cell center, area, and stain intensities
Path to molecules file
Path to segmentations CSV
Type of cell spatial coordinate matrices to read; choose one or more of:
“centroids”: cell centroids in pixel coordinate space
“segmentations”: cell segmentations in pixel coordinate space
Type of molecule spatial coordinate matrices to read; choose one or more of:
“pixels”: molecule coordinates in pixel space
Type of available metadata to read; choose zero or more of:
“Area”: number of pixels in cell segmentation
“fov”: cell's fov
“Mean.MembraneStain”: mean membrane stain intensity
“Mean.DAPI”: mean DAPI stain intensity
“Mean.G”: mean green channel stain intensity
“Mean.Y”: mean yellow channel stain intensity
“Mean.R”: mean red channel stain intensity
“Max.MembraneStain”: max membrane stain intensity
“Max.DAPI”: max DAPI stain intensity
“Max.G”: max green channel stain intensity
“Max.Y”: max yellow stain intensity
“Max.R”: max red stain intensity
Filter molecules that match provided string
Filter genes from cell x gene matrix that match provided string
Only load in select FOVs. Nanostring SMI data contains 30 total FOVs.
If the counts matrix should be built from molecule coordinates for a specific segmentation; One of:
“Nuclear”: nuclear segmentations
“Cytoplasm”: cell cytoplasm segmentations
“Membrane”: cell membrane segmentations
If TRUE, only load molecules within a cell
Name to store FOV as
Name to store expression matrix as
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")
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")