createGiottoMerscopeObject: Create Vizgen MERSCOPE Giotto Object

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

Create Vizgen MERSCOPE Giotto Object

Description

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

Usage

createGiottoMerscopeObject(
  merscope_dir,
  data_to_use = c("subcellular", "aggregate"),
  FOVs = NULL,
  poly_z_indices = 1:7,
  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

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)

Value

a giotto object

Functions

• createGiottoMerscopeObject_subcellular(): Create giotto object with 'subcellular' workflow

• createGiottoMerscopeObject_aggregate(): Create giotto object with 'aggregate' workflow

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.