Create Vizgen MERSCOPE Giotto Object

Source: R/convenience_general.R

Given the path to a MERSCOPE experiment directory, creates a Giotto object. Supports both Parquet and HDF5 cell boundary formats (v2). Features automatic 2D vs 3D architecture detection with vertex validation.

createGiottoMerscopeObject(
  merscope_dir,
  version = 1,
  data_to_use = c("subcellular", "aggregate"),
  FOVs = NULL,
  polygon_format = c("parquet", "hdf5"),
  poly_z_indices = NULL,
  flip_axis = c("none", "y", "x", "both"),
  spat_unit = "cell",
  calculate_overlap = TRUE,
  overlap_to_matrix = TRUE,
  aggregate_stack = TRUE,
  aggregate_stack_param = list(summarize_expression = "sum", summarize_locations =
    "mean", new_spat_unit = "cell"),
  split_keyword = c("Blank"),
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

.createGiottoMerscopeObject_subcellular(
  data_list,
  version = 1,
  flip_axis = c("none", "y", "x", "both"),
  spat_unit = "cell",
  calculate_overlap = TRUE,
  overlap_to_matrix = TRUE,
  aggregate_stack = TRUE,
  aggregate_stack_param = list(summarize_expression = "sum", summarize_locations =
    "mean"),
  split_keyword = c("Blank"),
  instructions = NULL,
  cores = NA,
  verbose = TRUE
)

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

Arguments

merscope_dir

full path to the exported merscope directory

version

integer. Version of logic to use (1 = Legacy/Original, 2 = New/Optimized)

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)

polygon_format

format of the boundary files, either 'parquet' or 'hdf5' (v2 only)

poly_z_indices

which z-indices to use for the polygons (Default 0:6 for v2, 1:7 for v1)

flip_axis

character. Version 2 only. Axis along which to reflect polygon vertices and transcript coordinates after loading: "none" (default, data read as-is), "y", "x", or "both". The reflection origin is the midpoint of the transcript coordinate range so both layers stay registered. Silently forced to "none" for version = 1, which handles orientation internally via polygon_mask_list_params (flip_vertical = TRUE).

spat_unit

character. Name assigned to the cell spatial unit (default "cell"). Controls the polygon layer name when a single Z-plane is present and serves as the default new_spat_unit in aggregate_stack_param when that field is not already supplied.

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

split_keyword

character vector of keywords to separate feature detections (e.g. "Blank")

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

Functions

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

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