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 = FALSE
)Arguments
- gpolygons
giotto polygons
- polygon_mask_list_params
list parameters for
createGiottoPolygonsFromMask- polygon_dfr_list_params
list parameters for
createGiottoPolygonsFromDfr- gpoints
giotto points
- cell_metadata
cell annotation metadata
- feat_metadata
feature annotation metadata for each unique feature
- spatial_network
list of spatial network(s)
- spatial_network_name
list of spatial network name(s)
- spatial_grid
list of spatial grid(s)
- spatial_grid_name
list of spatial grid name(s)
- spatial_enrichment
list of spatial enrichment score(s) for each spatial region
- spatial_enrichment_name
list of spatial enrichment name(s)
- dimension_reduction
list of dimension reduction(s)
- nn_network
list of nearest neighbor network(s)
- images
list of images
- largeImages
deprecated
- largeImages_list_params
image params when loading largeImages as list
- instructions
list of instructions or output result from
createGiottoInstructions- cores
how many cores or threads to use to read data if paths are provided
- verbose
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)
Examples
x_gpolygons <- GiottoData::loadSubObjectMini("giottoPolygon")
x_gpoints <- GiottoData::loadSubObjectMini("giottoPoints")
createGiottoObjectSubcellular(
gpolygons = x_gpolygons,
gpoints = x_gpoints
)
#> python already initialized in this session
#> active environment : 'giotto_env'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
#> polygonlist is not a list
#> [ cell ] Process polygon info...
#> There are non numeric or integer columns for the spatial location
#> input at column position(s): 1
#> The first non-numeric column will be considered as a cell ID
#> to test for consistency with the expression matrix
#> Other non numeric columns will be removed
#> Setting spatial locations [aggregate] raw
#> pointslist is not a list
#> [ rna ] Process point info...
#> python already initialized in this session
#> active environment : 'giotto_env'
#> python version : 3.10
#> checking default envname 'giotto_env'
#> a system default python environment was found
#> Using python path:
#> "/usr/share/miniconda/envs/giotto_env/bin/python"
#> An object of class giotto
#> [SUBCELLULAR INFO]
#> polygons : aggregate
#> features : rna
#> [AGGREGATE INFO]
#> spatial locations ----------------
#> [aggregate] raw
#>
#>
#> Use objHistory() to see steps and params used