View source: R/formatTxSpots.R
formatTxTech | R Documentation |
To preset parameters such as spatialCoordsNames
, gene_col
,
cell_col
, and phred_col
that are standard for the output of the
technology.
formatTxTech(
data_dir,
tech = c("Vizgen", "Xenium", "CosMX"),
dest = c("rowGeometry", "colGeometry"),
z = "all",
min_phred = 20,
split_cell_comps = FALSE,
z_option = c("3d", "split"),
flip = FALSE,
file_out = NULL,
BPPARAM = SerialParam(),
return = TRUE
)
addTxTech(
sfe,
data_dir,
sample_id = 1L,
tech = c("Vizgen", "Xenium", "CosMX"),
z = "all",
min_phred = 20,
split_cell_comps = FALSE,
z_option = c("3d", "split"),
flip = FALSE,
file_out = NULL,
BPPARAM = SerialParam()
)
data_dir |
Top level output directory. |
tech |
Which technology whose output to read, must be one of "Vizgen", "Xenium", or "CosMX" though more technologies may be added later. |
dest |
Where in the SFE object to store the spot geometries. This affects how the data is processed. Options:
|
z |
Which z-planes to read. Always "all" for Xenium where the z coordinates are not discrete. |
min_phred |
Minimum Phred score to keep spot. By default 20, the conventional threshold indicating "acceptable", meaning that there's 1 chance that the spot was decoded in error. |
split_cell_comps |
Only relevant to CosMX whose transcript spot file
assigns the spots to cell components. Setting this argument to |
z_option |
What to do with z coordinates. "3d" is to construct 3D geometries. "split" is to create a separate 2D geometry for each z-plane so geometric operations are fully supported but some data wrangling is required to perform 3D analyses. When the z coordinates are not integers, 3D geometries will always be constructed since there are no z-planes to speak of. This argument does not apply when 'spatialCoordsNames' has length 2. |
flip |
Logical, whether to flip the geometry to match image. Here the y
coordinates are simply set to -y, so the original bounding box is not
preserved. This is consistent with |
file_out |
Name of file to save the geometry or raster to disk. Especially when the geometries are so large that it's unwieldy to load everything into memory. If this file (or directory for multiple files) already exists, then the existing file(s) will be read, skipping the processing. When writing the file, extensions supplied are ignored and extensions are determined based on 'dest'. |
BPPARAM |
|
return |
Logical, whether to return the geometries in memory. This does not depend on whether the geometries are written to file. Always 'FALSE' when 'dest = "colGeometry"'. |
sfe |
A 'SpatialFeatureExperiment' object. |
sample_id |
Which sample in the SFE object the transcript spots should be added to. |
The 'sf' data frame, or path to file where geometries are written if 'return = FALSE'.
library(SFEData)
fp <- tempdir()
dir_use <- XeniumOutput("v2", file_path = file.path(fp, "xenium_test"))
fn_tx <- formatTxTech(dir_use, tech = "Xenium", flip = TRUE, return = FALSE,
file_out = file.path(dir_use, "tx_spots.parquet"))
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