Compute Highly Variable Genes

exportGiottoViewer()

Compute highly variable genes.

exportGiottoViewer(
    gobject,
     output_directory = NULL,
    spat_enr_names = NULL,
    factor_annotations = NULL,
    numeric_annotations = NULL,
    dim_reductions,
    dim_reduction_names,
    expression_values = c("scaled", "normalized", "custom"),
    dim_red_rounding = NULL,
    dim_red_rescale = c(-20, 20),
    expression_rounding = 2,
    overwrite_dir = T,
    verbose = T
)

Arguments

gobject	giotto object
output_directory	directory where to save the files
spat_enr_names	spatial enrichment results to include for annotations
factor_annotations	Giotto cell annotations to view as factor
numeric_annotations	Giotto cell annotations to view as numeric
dim_reductions	high level dimension reductions to view
dim_reduction_names	specific dimension reduction names
expression_values	expression values to use in Viewer
dim_red_rounding	numerical indicating how to round the coordinates
dim_red_rescale	numerical to rescale the coordinates
expression_rounding	numerical indicating how to round the expression data
overwrite_dir	overwrite files in the directory if it already existed
verbose	be verbose

Value

Writes the necessary output to use in Giotto Viewer.

Details

Giotto Viewer expects the results from Giotto Analyzer in a specific format, which is provided by this function. To include enrichment results from createSpatialEnrich() include the provided spatial enrichment name (default PAGE or rank) and add the gene signature names (.e.g cell types) to the numeric annotations parameter.

Examples

if (FALSE) {

data(mini_giotto_single_cell)
exportGiottoViewer(mini_giotto_single_cell)

}