Giotto import functionalities for CosMx datasets. This function generates a `CosmxReader` instance that has convenient reader functions for converting individual pieces of CosMx data into Giotto-compatible representations when the params `cosmx_dir` and `fovs` (if only a subset is desired) are provided. A function that creates the full `giotto` object is also available. These functions should have all param values provided as defaults, but can be flexibly modified to do things such as look in alternative directories or paths.
importCosMx(
cosmx_dir = NULL,
slide = 1,
fovs = NULL,
micron = FALSE,
px2um = 0.12028,
poly_pref = "mask"
)CosMx output directory
numeric. Slide number. Defaults to 1
numeric. (optional) If provided, will load specific fovs. Otherwise, all FOVs will be loaded
logical. Whether to scale spatial information as micron instead of the default pixels
numeric. Scalefactor from pixels to micron. Defaults to 0.12028 based on `CosMx-ReadMe.html` info. May be different depending on dataset.
character. Either "csv" (default) or "mask". Which format of data to load as polygon info. "csv" will use vector polygons from the `polygons.csv`. "mask" will load the mask images from `CellLabels` directory.
CosmxReader object
Loading functions are generated after the `cosmx_dir` is added. Transcripts, expression, and metadata loading are all expected to be done from the top level of the directory. Loading of polys, and any image sets are expected to be from specific subdirectories containing only those images for the set of FOVs.
# Create a `CosmxReader` object
reader <- importCosMx()
if (FALSE) { # \dontrun{
# Set the cosmx_dir and fov parameters
path <- "path/to/cosmx/dir"
reader$cosmx_dir <- path
reader$fov <- c(1, 4)
plot(reader) # displays FOVs (top left corner) in px scale.
# Load polygons, transcripts, and images
polys <- reader$load_polys()
tx <- reader$load_transcripts()
imgs <- reader$load_images()
# polygons (mask) and images loading supports multiple filepaths
# This can be useful when loading AtoMx outputs
polys <- reader$load_polys(path = list.files(path,
pattern = "CellLabels_F",
recursive = TRUE,
full.names = TRUE
))
imgs <- reader$load_images(path = list.files(path,
pattern = "Composite_F",
recursive = TRUE,
full.names = TRUE
))
# Create a `giotto` object and add the loaded data
g <- giotto()
g <- setGiotto(g, tx[["rna"]])
g <- setGiotto(g, polys)
g <- addGiottoLargeImage(g, largeImages = imgs)
force(g)
} # }