SpatialExperiment object to Seurat object

Transfer SpatialExperiment object to a Seurat object for preparation for DR.SC model fitting.

simu_seuList(seu, annotated_label, spatial_coords= c("row", "col"),
                             NumBatches = 3, NumSpotsRatio=0.9, ngenes = 2000, sim_seed=1,
                             batch_facLoc=0.1, batch_facScale = 0.1)

Arguments

seu

seu is an object named Seurat, which can easily created by R package Seurat.

annotated_label

a string, the colname of annotations in meta.data of seu about spatial domains/cell types.

spatial_coords

a string vector, the spatial coordinates information in the metadata of seu, default as named "row" and "col".

NumBatches

an optional integer, the number of batches to simulate; default as 3.

NumSpotsRatio

a real between 0.1 to 1. It controls the number of spots for each data batch.

ngenes

sim_seed

batch_facLoc

an optional logical value, whether output the information.

batch_facScale

Details

The number of spots for each data batch is approximately 80%~100% of the number of spots in seu, the baseline seurat object.

Value

Return a Seurat object, where the spatial coordinates information is saved in the metadata of Seurat, named "row" and "col".

Author

Wei Liu

Note

nothing

See also

None

Examples

if (FALSE) {
  library(DR.SC)
  data("dlpfc151510")
  dlpfc151510
  head(dlpfc151510@meta.data)
  ## Remove the unannotated spots
  seu <- dlpfc151510[,!is.na(dlpfc151510$annotation)]
  seulist_sim <- simu_seuList(seu, annotated_label = 'annotation', NumBatches = 2,
                          NumSpotsRatio = 0.5,spatial_coords=c("row", "col"), ngenes=50)

  seulist_sim <- lapply(seulist_sim, AddCoord2Reduc)
  seulist_sim2 <- lapply(seulist_sim, function(x){
    Idents(x) <- factor(x$Group)
    return(x)
  } )

  library(patchwork)
  pList <- lapply(seulist_sim2, DimPlot, reduction = "position", pt.size = 2)
  wrap_plots(pList, nrow=1)
  }