Slide-Seq data

In this article, we’ll demonstrate how to load Slide-Seq data with semla. First, we need to load a Seurat object with Slide-Seq data. Here we’ll use a prepared Seurat object that can be install with the SeuratData R package.

See ?ReadSlideSeq for more information on how to load raw data.

library(semla)
library(SeuratData)
InstallData("ssHippo")

slide_seq <- LoadData("ssHippo")

Next, we can convert the Seurat object to make it compatible with semla using the UpdateSeuratForSemla function. Note that the Slide-Seq data doesn’t contain H&E images and therefore, all image related functionality of semla will be inaccessible. This includes the Feature Viewer and image alignment tools which requires H&E images to work.

slide_seq_semla <- UpdateSeuratForSemla(slide_seq)

Now we can use visualization functions from semla on our Slide-Seq data.

MapFeatures(slide_seq_semla, features = "nFeature_Spatial", colors = viridis::magma(n = 11, direction = -1)) & ThemeLegendRight()

Zoom in on Dentate gyrus:

MapFeatures(slide_seq_semla, features = "PROX1", colors = viridis::magma(n = 11, direction = -1),
            crop_area = c(0.35, 0.45, 0.7, 0.7)) & 
  ThemeLegendRight() &
  ggtitle("PROX1 expression in the Dentate Gyrus", subtitle = "")

Package versions

semla: 1.1.6

Session info

sessionInfo()

## R version 4.4.0 (2024-04-24)
## Platform: aarch64-apple-darwin20
## Running under: macOS Sonoma 14.5
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/Stockholm
## tzcode source: internal
## 
## attached base packages:
## [1] stats     graphics  grDevices datasets  utils     methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37       desc_1.4.3          R6_2.5.1           
##  [4] fastmap_1.2.0       xfun_0.47           cachem_1.1.0       
##  [7] knitr_1.48          htmltools_0.5.8.1   rmarkdown_2.28     
## [10] lifecycle_1.0.4     cli_3.6.3           sass_0.4.9         
## [13] pkgdown_2.1.0       textshaping_0.4.0   jquerylib_0.1.4    
## [16] renv_1.0.2          systemfonts_1.1.0   compiler_4.4.0     
## [19] rstudioapi_0.16.0   tools_4.4.0         ragg_1.3.3         
## [22] bslib_0.8.0         evaluate_0.24.0     yaml_2.3.10        
## [25] BiocManager_1.30.25 jsonlite_1.8.8      htmlwidgets_1.6.4  
## [28] rlang_1.1.4         fs_1.6.4

Last compiled: 18 September 2024