Reproducing the Application Note figures

This vignette shows how to reproduce the visualizations published in the dbVisuals Application Note. For a general introduction, see vignette("getting-started", package = "dbVisuals").

Install

install.packages("dbVisuals")

# development version
install.packages("dbVisuals",
                 repos = c("https://dbverse-org.r-universe.dev",
                           "https://cloud.r-project.org"))

# rendering packages and database dependencies, from CRAN
install.packages(c("DBI", "duckdb", "rDeckgl", "rMosaic"))

The figures and benchmarks in the Application Note were made with dbVisuals 0.1.0 (commit 7f6eb52 of https://github.com/dbverse-org/dbVisuals).

Reproducing the published figures

The published in-situ panels need a GiottoDB DuckDB database holding cell polygons, cell centroids and transcript coordinates. The Application Note uses the 10x Genomics Atera In Situ Gene Expression, FFPE Human Breast Cancer preview dataset.

The two scripts below are in the repository under r-package/examples/. They are not installed with the package, and the large public input datasets are not bundled. Use the same release for the installed package and the cloned scripts.

Script	Renders
`03_dimred_concat.R`	UMAP / PCA dimension pairs linked to a `leiden_clus` bar
`06_in_situ_zoom_overlay_transcripts_interactive.R`	the published panel, with interactive ROI selection

Run them from a clone of the repository, with r-package/ as the working directory:

git clone --branch v0.1.0 https://github.com/dbverse-org/dbVisuals.git

03_dimred_concat.R needs the Giotto and GiottoData packages (see the Giotto Suite installation instructions) and downloads the mini Visium object. It needs no local database:

setwd("path/to/dbVisuals/r-package")
source("examples/03_dimred_concat.R")

For the in-situ script, point the environment at your data and run it from an interactive R session:

setwd("path/to/dbVisuals/r-package")
Sys.setenv(DBLENS_DEMO_DB = "/path/to/WTA_Preview_FFPE_Breast_Cancer_xenium.duckdb")
Sys.setenv(DBLENS_TRANSCRIPT_FILE = "/path/to/transcripts.parquet")
source("examples/06_in_situ_zoom_overlay_transcripts_interactive.R")

Neither variable is needed if the files sit in the working directory under their default names. Optional overrides: DBLENS_TRANSCRIPT_TABLE reads transcripts from a table inside the database instead of a file, and DBLENS_ROI_CELL_ID centres the region of interest on a specific cell.

Script 06 starts a Shiny app: dragging the select control re-queries only the transcripts inside the chosen region, and detail picks a nested sub-region. Under Rscript it prints the widget instead of launching Shiny. The published panel is a full-window capture of the resulting three-view layout. Missing expression or cell-type annotations are shown as unavailable, not simulated.

Install

Reproducing the published figures

See also