simulateOneGenePatternGiottoObject#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_genes.R#L3930

Description#

Create a simulated spatial pattern for one selected gnee

Usage#

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#

Argument

Description

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

list()

additional parameters for (re-)normalizing

Value#

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