GiottoDB

The goal of GiottoDB is to provide dbverse interoperability with objects from Giotto Suite for spatial omics data analysis in R.

Installation

# install.packages("pak")
pak::pak("giotto-suite/GiottoDB")

Example

library(GiottoDB)
library(GiottoData)
library(DBI)
library(duckdb)

# Load a small example Giotto object.
gobject <- GiottoData::loadGiottoMini("visium")

# Create GiottoDB object with a temporary local database.
db_path <- tempfile("giottodb-mini-", fileext = ".duckdb")
con <- DBI::dbConnect(duckdb::duckdb(), dbdir = db_path)
gdb <- as_giottodb(gobject, con = con)

# Preview the GiottoDB object
gdb
DBI::dbListTables(con)

# Disconnect from the database and clean up
DBI::dbDisconnect(con, shutdown = TRUE)