Create a giotto object from subcellular data#
Last Updated: Sep 07, 2023
Description#
Function to create a giotto object starting from subcellular polygon (e.g. cell) and points (e.g. transcripts) information
Usage#
createGiottoObjectSubcellular(
gpolygons = NULL,
polygon_mask_list_params = NULL,
polygon_dfr_list_params = NULL,
gpoints = NULL,
cell_metadata = NULL,
feat_metadata = NULL,
spatial_network = NULL,
spatial_network_name = NULL,
spatial_grid = NULL,
spatial_grid_name = NULL,
spatial_enrichment = NULL,
spatial_enrichment_name = NULL,
dimension_reduction = NULL,
nn_network = NULL,
images = NULL,
largeImages = NULL,
largeImages_list_params = NULL,
instructions = NULL,
cores = NA,
verbose = TRUE
)
Arguments#
|
giotto polygons |
|
list parameters for
|
|
list parameters for
|
|
giotto points |
|
cell annotation metadata |
|
feature annotation metadata for each unique feature |
|
list of spatial network(s) |
|
list of spatial network name(s) |
|
list of spatial grid(s) |
|
list of spatial grid name(s) |
|
list of spatial enrichment score(s) for each spatial region |
|
list of spatial enrichment name(s) |
|
list of dimension reduction(s) |
|
list of nearest neighbor network(s) |
|
list of images |
|
list of large images |
|
list of instructions or output
result from
|
|
how many cores or threads to use to read data if paths are provided |
|
be verbose when building Giotto object |
Details#
There are two different ways to create a Giotto Object with subcellular information: - Starting from polygons (spatial units e.g. cell) represented by a mask or dataframe file and giotto points (analyte coordinates e.g. transcripts) - Starting from polygons (spatial units e.g. cell) represented by a mask or dataframe file and raw intensity images (e.g. protein stains)
Value#
giotto object