spatialDE: spatialDE
In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

spatialDE

R Documentation

spatialDE

Description

Compute spatial variable genes with spatialDE method

Usage

spatialDE(
  gobject = NULL,
  feat_type = NULL,
  spat_unit = NULL,
  spat_loc_name = "raw",
  expression_values = c("raw", "normalized", "scaled", "custom"),
  size = c(4, 2, 1),
  color = c("blue", "green", "red"),
  sig_alpha = 0.5,
  unsig_alpha = 0.5,
  python_path = NULL,
  show_plot = NA,
  return_plot = NA,
  save_plot = NA,
  save_param = list(),
  default_save_name = "SpatialDE"
)

Arguments

`gobject`	Giotto object
`feat_type`	feature type
`spat_unit`	spatial unit
`spat_loc_name`	name for spatial locations
`expression_values`	gene expression values to use
`size`	size of plot
`color`	low/medium/high color scheme for plot
`sig_alpha`	alpha value for significance
`unsig_alpha`	alpha value for unsignificance
`python_path`	specify specific path to python if required
`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

Details

This function is a wrapper for the SpatialDE method originally implemented in python. See publication \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/nmeth.4636")}