simulateOneGenePatternGiottoObject: simulateOneGenePatternGiottoObject

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

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

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

Examples

    simulateOneGenePatternGiottoObject(gobject)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.