Create Vizgen MERSCOPE Giotto Object — createGiottoMerscopeObject • Giotto

Given the path to a MERSCOPE experiment directory, creates a Giotto object.

createGiottoMerscopeObject(
  merscope_dir,
  data_to_use = c("subcellular", "aggregate"),
  FOVs = NULL,
  poly_z_indices = seq(from = 1, to = 7),
  calculate_overlap = TRUE,
  overlap_to_matrix = TRUE,
  aggregate_stack = TRUE,
  aggregate_stack_param = list(summarize_expression = "sum", summarize_locations =
    "mean", new_spat_unit = "cell"),
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

.createGiottoMerscopeObject_subcellular(
  data_list,
  calculate_overlap = TRUE,
  overlap_to_matrix = TRUE,
  aggregate_stack = TRUE,
  aggregate_stack_param = list(summarize_expression = "sum", summarize_locations =
    "mean", new_spat_unit = "cell"),
  cores = NA,
  verbose = TRUE
)

.createGiottoMerscopeObject_aggregate(data_list, cores = NA, verbose = TRUE)

Arguments

merscope_dir: full path to the exported merscope directory
data_to_use: which of either the 'subcellular' or 'aggregate' information to use for object creation
FOVs: which FOVs to use when building the subcellular object. (default is NULL) NULL loads all FOVs (very slow)
calculate_overlap: whether to run calculateOverlapRaster
overlap_to_matrix: whether to run overlapToMatrix
aggregate_stack: whether to run aggregateStacks
aggregate_stack_param: params to pass to aggregateStacks
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
data_list: list of loaded data from load_merscope_folder

Value

a giotto object

Details

[Expected Directory] This function generates a giotto object when given a link to a MERSCOPE output directory. It expects the following items within the directory where the bolded portions are what this function matches against:

cell_boundaries (folder .hdf5 files)
images (folder of .tif images and a scalefactor/transfrom table)
cell_by_gene.csv (file)
cell_metadatafov_positions_file.csv (file)
detected_transcriptsmetadata_file.csv (file)

Functions

.createGiottoMerscopeObject_subcellular(): Create giotto object with 'subcellular' workflow
.createGiottoMerscopeObject_aggregate(): Create giotto object with 'aggregate' workflow