gbspatial

The goal of gbspatial is to provide functions useful for spatial transcriptomics data analysis.

Installation

You can install the development version of gbspatial from GitHub with:

#devtools::install_github("gbarisano/gbspatial")
#OR
#pak::pak("gbarisano/gbspatial")
library(gbspatial)

Examples

PlotFOVSegmentation

PlotFOVSegmentation(seurat_obj = my_spatial_data,
                    fill = "updated_celltype",
                    img_dir= Sys.glob(file.path("data/DecodedFiles","*","*","CellStatsDir","CellComposite")),
                    fov_pos_file = Sys.glob(file.path("data/flatFiles", "*","*fov_positions_file.csv.gz")),
                    alpha=0.8)
#> Loading FOV positions for image 'TMA1' from: data/flatFiles/TMA1/TMA1_fov_positions_file.csv.gz
#> Loading FOV positions for image 'TMA2' from: data/flatFiles/TMA2/TMA2_fov_positions_file.csv.gz
#> Processing Image: TMA1
#>   -> Found 2 unique FOVs in image 'TMA1'.
#>   -> Rendering FOV: 1
#> Warning: Not validating FOV objects
#> Not validating FOV objects
#> Not validating FOV objects
#> Warning: Not validating Seurat objects
#> Not validating Seurat objects

#> Saved: ./FOV_1_TMA1_segmentation.png
#>   -> Rendering FOV: 2
#> Warning: Not validating FOV objects
#> Warning: Not validating FOV objects
#> Not validating FOV objects
#> Warning: Not validating Seurat objects
#> Not validating Seurat objects

#> Saved: ./FOV_2_TMA1_segmentation.png
#> Processing Image: TMA2
#>   -> Found 2 unique FOVs in image 'TMA2'.
#>   -> Rendering FOV: 1
#> Warning: Not validating Seurat objects
#> Warning: Not validating FOV objects
#> Not validating FOV objects
#> Not validating FOV objects
#> Warning: Not validating Seurat objects

#> Saved: ./FOV_1_TMA2_segmentation.png
#>   -> Rendering FOV: 2
#> Warning: Not validating Seurat objects
#> Warning: Not validating FOV objects
#> Not validating FOV objects
#> Not validating FOV objects
#> Warning: Not validating Seurat objects

#> Saved: ./FOV_2_TMA2_segmentation.png
#> Pipeline complete.
knitr::include_graphics("FOV_1_TMA1_segmentation.png")

knitr::include_graphics("FOV_2_TMA1_segmentation.png")

knitr::include_graphics("FOV_1_TMA2_segmentation.png")

knitr::include_graphics("FOV_2_TMA2_segmentation.png")