Create Simulated Spatial Pattern

simulateOneGenePatternGiottoObject()

Create a simulated spatial pattern for one selected gene.

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

A reprocessed Giotto object for which one gene has a forced spatial pattern.