showPatternGenes: showPatternGenes

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

show genes correlated with spatial patterns

Usage

showPatternGenes(
  gobject,
  spatPatObj,
  dimension = 1,
  top_pos_genes = 5,
  top_neg_genes = 5,
  point_size = 1,
  return_DT = FALSE,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "showPatternGenes"
)

Arguments

gobject	giotto object
spatPatObj	Output from detectSpatialPatterns
dimension	dimension to plot genes for.
top_pos_genes	Top positively correlated genes.
top_neg_genes	Top negatively correlated genes.
point_size	size of points
return_DT	if TRUE, it will return the data.table used to generate the plots
show_plot	show plot
return_plot	return ggplot object
save_plot	directly save the plot [boolean]
save_param	list of saving parameters, see showSaveParameters
default_save_name	default save name for saving, don't change, change save_name in save_param

Value

ggplot

Examples

    showPatternGenes(gobject)

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