showPatternGenes: showPatternGenes
In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

showPatternGenes

R Documentation

showPatternGenes

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