Preamble

Dependencies

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library(ggplot2)
library(RColorBrewer)
library(ExperimentHub)
library(SpatialExperiment)
library(STexampleData)

Molecule-based dataset

Setup

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eh <- ExperimentHub()
q <- query(eh, "MERFISH")
df <- eh[["EH7546"]]

Wrangling

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# extract cell metadata
i <- seq_len(9)
cd <- data.frame(df[, i], row.names = 1)

# set sample identifiers
id <- grep("Bregma", names(cd))
names(cd)[id] <- "sample_id"

# rename spatial coordinates
xy <- grep("Centroid", names(cd))
xy <- names(cd)[xy] <- c("x", "y")

# simplify annotations
cd$cluster_id <- cd$Cell_class
for (. in c("Endothelial", "OD Mature", "OD Immature"))
  cd$cluster_id[grep(., cd$cluster_id)] <- .

# extract & sparsify assay data
y <- data.frame(df[, -i], row.names = df[, 1])
y <- as(t(as.matrix(y)), "dgCMatrix")

# construct SPE
(spe <- SpatialExperiment(
  assays = list(exprs  = y),
  spatialCoordsNames = xy,
  colData = cd))

class: SpatialExperiment 
dim: 161 73655 
metadata(0):
assays(1): exprs
rownames(161): Ace2 Adora2a ... Ucn3 Vgf
rowData names(0):
colnames(73655): 6749ccb4-2ed1-4029-968f-820a287f43c8
  6cac74bd-4ea7-4701-8701-42563cc65eb8 ...
  6b666f81-7b73-4100-9e02-b5381b39f0f3
  fdcddd97-7701-462a-b48f-979111245bd5
colData names(7): Animal_ID Animal_sex ... Neuron_cluster_ID cluster_id
reducedDimNames(0):
mainExpName: NULL
altExpNames(0):
spatialCoords names(2) : x y
imgData names(0):

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gg <- data.frame(spatialCoords(spe), colData(spe))
pal <- brewer.pal(length(unique(gg$cluster_id)), "Paired")
ggplot(gg, aes(x, y, col = cluster_id)) +
  facet_wrap(~ sample_id, scales = "free") +
  geom_point(size = 0.1) + scale_color_manual(values = pal) +
  guides(col = guide_legend(override.aes = list(size = 2))) +
  theme_void() + theme(legend.key.size = unit(0.5, "lines"))

Save data

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# Define the directory and file paths
dir_path <- "../data"

# Check if the directory exists, and create it if it doesn't
if (!dir.exists(dir_path)) {
  dir.create(dir_path)
}

saveRDS(spe, "../data/spe.rds")

Appendix

Session info

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sessionInfo()

R version 4.3.1 (2023-06-16)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.7.2

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

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/Zurich
tzcode source: internal

attached base packages:
[1] stats4    stats     graphics  grDevices datasets  utils     methods  
[8] base     

other attached packages:
 [1] MerfishData_1.2.0           EBImage_4.42.0             
 [3] STexampleData_1.8.0         SpatialExperiment_1.10.0   
 [5] SingleCellExperiment_1.22.0 SummarizedExperiment_1.30.2
 [7] Biobase_2.60.0              GenomicRanges_1.52.1       
 [9] GenomeInfoDb_1.36.4         IRanges_2.34.1             
[11] S4Vectors_0.38.2            MatrixGenerics_1.12.3      
[13] matrixStats_1.5.0           ExperimentHub_2.8.1        
[15] AnnotationHub_3.8.0         BiocFileCache_2.8.0        
[17] dbplyr_2.3.4                BiocGenerics_0.46.0        
[19] RColorBrewer_1.1-3          ggplot2_3.5.1              

loaded via a namespace (and not attached):
 [1] DBI_1.2.3                     bitops_1.0-9                 
 [3] rlang_1.1.4                   magrittr_2.0.3               
 [5] compiler_4.3.1                RSQLite_2.3.9                
 [7] DelayedMatrixStats_1.22.6     fftwtools_0.9-11             
 [9] png_0.1-8                     vctrs_0.6.5                  
[11] pkgconfig_2.0.3               crayon_1.5.3                 
[13] fastmap_1.2.0                 magick_2.8.5                 
[15] XVector_0.40.0                labeling_0.4.3               
[17] scuttle_1.10.3                promises_1.3.2               
[19] rmarkdown_2.29                purrr_1.0.2                  
[21] bit_4.5.0.1                   xfun_0.50                    
[23] zlibbioc_1.46.0               cachem_1.1.0                 
[25] beachmat_2.16.0               jsonlite_1.8.9               
[27] blob_1.2.4                    later_1.4.1                  
[29] rhdf5filters_1.12.1           DelayedArray_0.26.7          
[31] Rhdf5lib_1.22.1               BiocParallel_1.34.2          
[33] interactiveDisplayBase_1.38.0 jpeg_0.1-10                  
[35] tiff_0.1-12                   parallel_4.3.1               
[37] R6_2.5.1                      limma_3.56.2                 
[39] Rcpp_1.0.13-1                 knitr_1.49                   
[41] R.utils_2.12.3                httpuv_1.6.15                
[43] Matrix_1.5-4.1                tidyselect_1.2.1             
[45] rstudioapi_0.15.0             abind_1.4-8                  
[47] yaml_2.3.10                   codetools_0.2-19             
[49] curl_6.1.0                    lattice_0.22-6               
[51] tibble_3.2.1                  shiny_1.10.0                 
[53] withr_3.0.2                   KEGGREST_1.40.1              
[55] evaluate_1.0.1                Biostrings_2.68.1            
[57] pillar_1.10.1                 BiocManager_1.30.25          
[59] filelock_1.0.3                renv_1.0.11                  
[61] generics_0.1.3                RCurl_1.98-1.16              
[63] BiocVersion_3.17.1            sparseMatrixStats_1.12.2     
[65] munsell_0.5.1                 scales_1.3.0                 
[67] xtable_1.8-4                  glue_1.8.0                   
[69] tools_4.3.1                   locfit_1.5-9.10              
[71] rhdf5_2.44.0                  grid_4.3.1                   
[73] DropletUtils_1.20.0           AnnotationDbi_1.62.2         
[75] edgeR_3.42.4                  colorspace_2.1-1             
[77] GenomeInfoDbData_1.2.10       HDF5Array_1.28.1             
[79] cli_3.6.3                     rappdirs_0.3.3               
[81] S4Arrays_1.0.6                dplyr_1.1.4                  
[83] gtable_0.3.6                  R.methodsS3_1.8.2            
[85] digest_0.6.37                 dqrng_0.4.1                  
[87] farver_2.1.2                  rjson_0.2.23                 
[89] htmlwidgets_1.6.4             memoise_2.0.1                
[91] htmltools_0.5.8.1             R.oo_1.27.0                  
[93] lifecycle_1.0.4               httr_1.4.7                   
[95] mime_0.12                     bit64_4.5.2