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
)
giotto object
directory where to save the files
spatial enrichment results to include for annotations
giotto cell annotations to view as factor
giotto cell annotations to view as numeric
high level dimension reductions to view
specific dimension reduction names
expression values to use in Viewer
numerical indicating how to round the coordinates
numericals to rescale the coordinates
numerical indicating how to round the expression data
overwrite files in the directory if it already existed
be verbose
writes the necessary output to use in Giotto Viewer
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.
if (FALSE) {
data(mini_giotto_single_cell)
exportGiottoViewer(mini_giotto_single_cell)
}