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" )
| 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 |
| default_save_name | default save name for saving, don't change, change save_name in save_param |
a list of data.frames with results and plot (optional)
This function is a wrapper for the SpatialDE method implemented in the ...