I speculate that in practice, the most common use of the transcript spots is
visualization, and only a few genes can be visualized at a time or the spots
will overcrowd. Then it doesn't make sense to load the transcript spots of
all genes into memory as they can take up a lot of memory. The function
readSelectTx
reads transcript spots of select genes into R, and the
function addSelectTx
adds them to rowGeometries
of the SFE
object.
Arguments
- file
File path of a GeoParquet file (e.g. already reformatted with the
formatTxSpots
oraddTxSpots
function, should have already flipped to match image if necessary).- gene_select
Character vector of a subset of genes. If
NULL
, then all genes that have transcript spots are added. Only relevant when reading data from formatted files on disk. If specified, thenreturn = TRUE
.- z
Index of z plane to read. Can be "all" to read all z-planes into MULTIPOINT geometries with XYZ coordinates. If z values are not integer, then spots with all z values will be read.
- 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.
- sfe
A `SpatialFeatureExperiment` object.
- sample_id
Which sample in the SFE object the transcript spots should be added to.
- swap_rownames
Name of a column in
rowData(sfe)
to use as gene identifiers in place of the actual row names. In some cases this may be needed to match each transcript spot MULTIPOINT geometry to rows ofsfe
.
Value
When there are multipel parquet files to be read, a list of sf data
frames with MULTIPOINT geometry for genes selected. When there is only one
file, then one sf data frame. For addSelectTx
, an SFE object with
the transcript spots of the selected genes added.
Note
The GDAL Parquet driver is required for this function, though not for
other functions that work with GeoParquet files. GDAL Parquet driver has
been supported since GDAL 3.5.0, but is not part of the default
installation. The z
and z_option
arguments are there since
the file names contain z-plane information when relevant.
See the GDAL documentation
page for the Parquet driver.
Examples
library(SFEData)
if (gdalParquetAvailable()) {
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"))
gene_select <- c("ACE2", "BMX")
df <- readSelectTx(fn_tx, gene_select)
sfe <- readXenium(dir_use)
sfe <- addSelectTx(sfe, fn_tx, head(rownames(sfe), 5), swap_rownames = "Symbol")
unlink(dir_use, recursive = TRUE)
}