Compute Spatial Variables With SpatialDE Method

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 insignificance
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). There are 3 fields reported per gene: LLR, pval, qval. LLR is log-likelihood of model, useful for creating a whole ranking of genes unambiguously. P-val, Q-val are useful for cut-off based approach to filtering the spatial genes.

Details

This is one of methods that Giotto supports to search for spatially variable genes. This function is a wrapper for the SpatialDE method implemented in the SpatialDE function. The input is a gene expression matrix. There are 4 version of expression matrix (indicated by expression_values). Raw version (in counts) is recommended. SpatialDE performs library size normalization (by default) if raw expression is used. Otherwise, one can also use “normalized” and skip SpatialDE normalization step.

There are no other parameters required. The parameters color, sig_alpha, unsig_alpha are used for plotting the Fraction spatial variance vs Adj. P-value SpatialDE GitHub, and is optional. To disable this FSV vs. Adj P-value plot, show_plot is set to NA (default). The parameters return_plot, save_plot, save_param are for saving the results automatically to disk (default values are NA). They are attached to every function (see CreateGiottoInstructions()).