pancreas_sub: A subsetted version of mouse 'pancreas' datasets

In zh542370159/SCP: Single Cell Pipeline

A subsetted version of mouse 'pancreas' datasets

Description

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

## Not run: 
if (interactive()) {
  library(Seurat)
  library(reticulate)
  check_Python("scvelo")
  scv <- import("scvelo")
  adata <- scv$datasets$pancreas()
  pancreas <- adata_to_srt(adata)
  set.seed(11)
  pancreas_sub <- subset(pancreas, cells = sample(colnames(pancreas), size = 1000))
  pancreas_sub <- pancreas_sub[rowSums(pancreas_sub@assays$RNA@counts) > 0, ]
  pancreas_sub[["CellType"]] <- pancreas_sub[["clusters_coarse"]]
  pancreas_sub[["SubCellType"]] <- pancreas_sub[["clusters"]]
  pancreas_sub[["clusters_coarse"]] <- pancreas_sub[["clusters"]] <- NULL
  pancreas_sub[["Phase"]] <- ifelse(pancreas_sub$S_score > pancreas_sub$G2M_score, "S", "G2M")
  pancreas_sub[["Phase"]][apply(pancreas_sub[[]][, c("S_score", "G2M_score")], 1, max) < 0, ] <- "G1"
  pancreas_sub[["Phase", drop = TRUE]] <- factor(pancreas_sub[["Phase", drop = TRUE]], levels = c("G1", "S", "G2M"))
  pancreas_sub[["PCA"]] <- pancreas_sub[["X_pca"]]
  pancreas_sub[["UMAP"]] <- pancreas_sub[["X_umap"]]
  pancreas_sub[["X_umap"]] <- pancreas_sub[["X_pca"]] <- NULL
  VariableFeatures(pancreas_sub) <- rownames(pancreas_sub[["RNA"]])[which(pancreas_sub[["RNA"]]@meta.features$highly_variable_genes == "True")]
  # usethis::use_data(pancreas_sub, compress = "xz")
}

## End(Not run)

zh542370159/SCP documentation built on Nov. 22, 2023, 2:34 a.m.