spatialDE

Compute spatial variable genes with spatialDE method

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

Value

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

Details

This function is a wrapper for the SpatialDE method implemented in the ...