A subsetted version of mouse 'pancreas' datasets

Mouse pancreatic endocrinogenesis dataset from Bastidas-Ponce et al. (2019). A total of 1000 cells were downsampled to form the pancreas_sub dataset.

Format

A Seurat object.

Source

https://scvelo.readthedocs.io/scvelo.datasets.pancreas/ https://github.com/theislab/scvelo_notebooks/raw/master/data/Pancreas/endocrinogenesis_day15.h5ad

Examples

if (FALSE) { # \dontrun{
if (interactive()) {
  library(Seurat)
  library(reticulate)
  check_python("scvelo")
  scv <- import("scvelo")
  adata <- scv$datasets$pancreas()
  pancreas <- adata_to_srt(adata)
  set.seed(11)
  cells <- sample(colnames(pancreas), size = 1000)
  pancreas_sub <- pancreas[, cells]
  pancreas_sub <- pancreas_sub[Matrix::rowSums(
    GetAssayData5(
      pancreas_sub,
      slot = "counts"
    )
  ) > 0, ]
  pancreas_sub[["CellType"]] <- pancreas_sub[["clusters_coarse"]]
  pancreas_sub[["SubCellType"]] <- pancreas_sub[["clusters"]]
  pancreas_sub[["clusters_coarse"]] <- pancreas_sub[["clusters"]] <- NULL
  pancreas_sub[["Phase"]] <- ifelse(
    pancreas_sub$S_score > pancreas_sub$G2M_score,
    "S",
    "G2M"
  )
  pancreas_sub[["Phase"]][apply(
    pancreas_sub[[]][, c("S_score", "G2M_score")],
    1,
    max
  ) < 0, ] <- "G1"
  pancreas_sub[["Phase", drop = TRUE]] <- factor(
    pancreas_sub[["Phase", drop = TRUE]],
    levels = c("G1", "S", "G2M")
  )
  pancreas_sub$CellType <- gsub("_", "-", pancreas_sub$CellType)
  pancreas_sub$CellType <- gsub(" ", "-", pancreas_sub$CellType)
  pancreas_sub$SubCellType <- gsub("_", "-", pancreas_sub$SubCellType)
  pancreas_sub$SubCellType <- gsub(" ", "-", pancreas_sub$SubCellType)
  pancreas_sub <- Seurat::NormalizeData(pancreas_sub, verbose = FALSE)
  pancreas_sub <- Seurat::FindVariableFeatures(
    pancreas_sub,
    verbose = FALSE
  )
  pancreas_sub <- Seurat::ScaleData(pancreas_sub, verbose = FALSE)
  pancreas_sub <- Seurat::RunPCA(pancreas_sub, verbose = FALSE)
  pancreas_sub <- Seurat::RunUMAP(
    pancreas_sub,
    dims = 1:30,
    verbose = FALSE
  )
  pancreas_sub <- Seurat::RunTSNE(
    pancreas_sub,
    dims = 1:30,
    verbose = FALSE
  )
  pancreas_sub <- RunDEtest(
    pancreas_sub,
    group_by = "CellType"
  )
  usethis::use_data(
    pancreas_sub,
    compress = "xz",
    overwrite = TRUE
  )
}
} # }