Updating spatialLIBD From SingleCellExperiment to VisiumExperiment classes spatialLIBD version 1.1.7 Brenda Pardo @PardoBree bpardo99 2020-12-17 #spatialLIBD 1

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

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

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

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

• 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

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

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

Using spatialLIBD functions on DLPFC VisiumExperiment object Version 1.1.7 Bioconductor 3.12 9

• 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

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

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