Updating spatialLIBD: from SingleCellExperiment to VisiumExperiment classes

Updates on the package spatialLIBD that allow it to use objects of the VisiumExperiment class, which is designed to specifically store spatial transcriptomics data.
These slides were designed for EuroBioC202.

Transcript

1. Updating spatialLIBD From SingleCellExperiment to VisiumExperiment classes spatialLIBD version 1.1.7 Brenda Pardo @PardoBree bpardo99 2020-12-17 #spatialLIBD 1
2. Transcriptome-scale spatial gene expression in the Human Dorsolateral Prefrontal Cortex 1. Identification of layer-enriched genes in human cortex. 2. Spatial registration of single nucleus RNA-seq data from human cortex. 3. Layer-enriched expression of genes associated with brain disorders. Maynard, Collado-Torres, et al, bioRxiv, 2020 2
3. What is spatialLIBD? Functions for 1. accessing the spatial transcriptomics data, 2. visualizing the spot-level spatial gene expression data and clusters, and 3. inspecting the data interactively. Maynard, Collado-Torres, et al, bioRxiv, 2020 3
4. SingleCellExperiment SpatialExperiment VisiumExperiment spatialCoords SLOTS METHODS show spatialCoords spatialCoords<- SLOTS imagePaths inTissue scaleFactors METHODS show imagePaths imagePaths<- isInTissue scaleFactors scaleFactors<- VisiumExperiment, a class for spatial transcriptomics data Dario Righelli and Davide Risso Version 1.0.0 https://doi.org/doi:10.18129/B9.bioc.SpatialExperiment 4
5. Updating spatialLIBD by using VisiumExperiment for multiple samples • The function fetch_data(), retrieves a VisiumExperiment object containing DLPFC spatial transcriptomics data. • The VisiumExperiment object contains scale factors and local image paths for multiple DLPFC tissue images. • The function for visualizing the histology image from Visium, geom_spatial(), was adapted to use VisiumExperiment objects. • Functions to visualize the gene expression (or any continuous variable) and clusters for one given sample at the spot-level where modified to use VisiumExperiment objects. 5
6. • VisiumExperiment class validity code checks that the image paths are local. • Download DLPFC images from URL, using BiocFileCashe, at the moment the VisiumExperiment object is created. • scaleFactors slot is designed to handle a single sample. • Must contain a list with names for the four scale factors: tissue_lowres_scalef, fiducial_diameter_fullres, tissue_hires_scalef and spot_diameter_fullres. Difficulties using VisiumExperiment class at spatialLIBD 6
7. Difficulties using VisiumExperiment class at spatialLIBD • scaleFactors contains • a list with the required four scale factors names. • a fifth list element with the full list of scale factors for all our samples. Version 1.1.7 Bioconductor 3.12 7
8. Difficulties using VisiumExperiment class at spatialLIBD • update_scaleFactors() updates scale factors for a given input sample ID. Version 1.1.7 Bioconductor 3.12 8
9. Using spatialLIBD functions on DLPFC VisiumExperiment object Version 1.1.7 Bioconductor 3.12 9
10. • Based on work with Helena L. Crowell, Lukas Weber and Dario Righelli • To move spatialLIBD graphical functions to new package. • Update spatialLIBD based on the new version of the SpatialExperiment package. • Application note about spatialLIBD. Future directions of spatialLIBD 10
11. Blog post at LIBD rstats club http://research.libd.org/ rstatsclub/2020/11/06/using- visiumexperiment-at- spatiallibd-package/#starting- internship-at-lieber-institute Check it out here! @PardoBree bpardo99 #spatialLIBD 11
12. Acknowledgements Lieber Institute Leonardo Collado-Torres Kristen R. Maynard Keri Martinowich Josh Stolz Abby Spangler JHU Biostatistics Dept Stephanie C. Hicks Lukas M. Weber 12