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Run Augur analysis

Source: R/celltype.R
leo.augur.Rd

We added functionality to subset srt obj so that you can compare differet group's results

Usage

leo.augur(
  srt,
  subset_col = NULL,
  subset_value = c("Control", "Inactive"),
  label_level = NULL,
  label_col = "Stage1",
  cell_type_col = "cell_anno",
  n_threads = 8,
  return = "plot"
)

Arguments

srt

Seurat object

subset_col

Character. Column in meta.data to subset by (e.g. "Stage1")

subset_value

Character vector. Values to retain in subset_col

label_level

Character vector. Factor level order for subset_col (default: same as subset_value)

label_col

Character. Column in meta.data used as label for Augur

cell_type_col

Character. Column in meta.data representing cell types

n_threads

Integer. Number of threads for parallel Augur computation

return

Character. If "plot" (default), returns a list of plot and data; otherwise returns raw Augur object

Value

If return = "plot", a list with plot (ggplot object) and dat (Augur result); else, Augur result only