simulateOneGenePatternGiottoObject — simulateOneGenePatternGiottoObject • Giotto

Create a simulated spatial pattern for one selected gnee

simulateOneGenePatternGiottoObject(
  gobject,
  pattern_name = "pattern",
  pattern_cell_ids = NULL,
  gene_name = NULL,
  spatial_prob = 0.95,
  gradient_direction = NULL,
  show_pattern = TRUE,
  pattern_colors = c(`in` = "green", out = "red"),
  ...
)

Arguments

gobject: giotto object
pattern_name: name of spatial pattern
pattern_cell_ids: cell ids that make up the spatial pattern
gene_name: selected gene
spatial_prob: probability for a high expressing gene value to be part of the spatial pattern
gradient_direction: direction of gradient
show_pattern: show the discrete spatial pattern
pattern_colors: 2 color vector for the spatial pattern
...: additional parameters for (re-)normalizing

Value

Reprocessed Giotto object for which one gene has a forced spatial pattern