inst/scripts/make-data-STARmapPLUS-mouseBrain.R

In lmweber/STdata: Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format

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# Script to create SpatialExperiment object of the STARmap PLUS mouse brain
# well 05. 
# Yixing Dong, updated Mar 2024
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# references:
# STARmap PLUS `raw_expression_pd.csv` and `spatial.csv` file were downloaded from
# \url{https://zenodo.org/records/8327576}

# in this script we download the STARmap PLUS data and reshape it into a 
# SpatialExperiment object

# First, we need to install the `SpatialExperimentIO` loader package that would 
# return Xenium as a `SpatialExperiment` object: 

# install.packages("devtools")
# devtools::install_github("estellad/SpatialExperimentIO")

# or with the version of the package on Bioconductor: 

# if (!requireNamespace("BiocManager", quietly=TRUE))
#   install.packages("BiocManager")
# BiocManager::install("SpatialExperimentIO", version = "devel")

library(SpatialExperiment)
library(SpatialExperimentIO)

# -------------
# Download data
# -------------
# Put the downloaded unzipped file into a folder. Make sure that two mandatory 
# files do exist. 
star_well05_path <- here::here("raw_data/star_well05")
star_folder <- list.files(star_well05_path, pattern = ".csv")
star_folder


# ------------------------
# Create SpatialExperiment
# ------------------------

star_spe <- readStarmapplusSXE(star_well05_path, return_type = "SPE")
star_spe

# ------------------
# Saving data object
# ------------------

# We save the data to file for upload to `r Biocpkg("ExperimentHub")`.
repath <- here::here(file.path("raw_rds", "STARmapPLUS_mouseBrain"))
dir.create(repath, showWarnings=FALSE, recursive=TRUE)
saveRDS(star_spe, file=file.path(here::here(repath, "STARmapPLUS_mouseBrain.rds")))