spatialDE: spatialDE

In RubD/Giotto: Spatial Single-Cell Transcriptomics Toolbox

spatialDE

Description

Compute spatial variable genes with spatialDE method

Usage

spatialDE(
  gobject = NULL,
  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
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 implemented in the ...

Value

a list of data.frames with results and plot (optional)

RubD/Giotto documentation built on April 29, 2023, 5:52 p.m.