readSelectTx: Read transcript spots of select genes

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Read transcript spots of select genes

Description

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.

Usage

readSelectTx(file, gene_select, z = "all", z_option = c("3d", "split"))

addSelectTx(
  sfe,
  file,
  gene_select,
  sample_id = 1L,
  z = "all",
  z_option = c("3d", "split"),
  swap_rownames = NULL
)

Arguments

file	File path of a GeoParquet file (e.g. already reformatted with the formatTxSpots or addTxSpots 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, then return = 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 of sfe.

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 <- tempfile()
    dir_use <- XeniumOutput("v2", file_path = fp)
    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)
    # RBioFormats null pointer error the first time
    try(sfe <- readXenium(dir_use))
    sfe <- readXenium(dir_use)
    sfe <- addSelectTx(sfe, fn_tx, head(rownames(sfe), 5), swap_rownames = "Symbol")
    unlink(dir_use, recursive = TRUE)
}

pachterlab/SpatialFeatureExperiment documentation built on Dec. 20, 2024, 3:41 a.m.