spatialDE#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/spatial_genes.R#L1844

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#

Argument

Description

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 `showSaveP arameters <#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 c(“\Sexpr[results=rd]{tools:::Rd_expr_doi(“#1”)}?, “10.1038/nmeth.4636?) list(“tools:::Rd_expr_doi(“10.1038/nmeth.4636”)?)

Value#

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