ggspavis

ggspavis provides visualization functions for spatial transcriptomics data, generating plots for datasets from the 10x Genomics Visium and other technological platforms in SpatialExperiment or SingleCellExperiment format.

Key Features:

• Spot plots: Generates spatial visualizations of transcriptomic data at spot resolution.
• Feature (molecule) plots: Creates visualizations showing the spatial distribution of specific molecules or features.
• Reduced dimension plots: Produces dimensionality reduction visualizations such as UMAP or t-SNE embeddings.
• Spot-level quality control plots: Generates QC visualizations assessing data quality at individual spot positions.
• Feature-level quality control plots: Creates QC visualizations evaluating quality metrics for individual features or genes.

Scientific Applications:

• Spatial transcriptomics data visualization: Enables exploratory data analysis and quality assessment of spatially resolved transcriptomic datasets from 10x Genomics Visium and compatible platforms.

Methodology:

The package accepts datasets in SpatialExperiment or SingleCellExperiment format and applies specialized plotting functions to generate spatial and non-spatial visualizations for quality control and data exploration.