readPolygonFilesVizgenHDF5

Read polygon info for all cells or for only selected FOVs from Vizgen HDF5 files. Data is returned as a list of giottoPolygons or data.tables of the requested z indices.

readPolygonFilesVizgenHDF5(
  boundaries_path,
  fovs = NULL,
  z_indices = 1L:7L,
  segm_to_use = 1L,
  custom_polygon_names = NULL,
  flip_x_axis = FALSE,
  flip_y_axis = TRUE,
  calc_centroids = FALSE,
  smooth_polygons = TRUE,
  smooth_vertices = 60L,
  set_neg_to_zero = FALSE,
  H5Fopen_flags = "H5F_ACC_RDWR",
  cores = determine_cores(),
  create_gpoly_parallel = TRUE,
  create_gpoly_bin = FALSE,
  verbose = TRUE,
  output = c("giottoPolygon", "data.table"),
  polygon_feat_types = NULL
)

Arguments

boundaries_path

path to the cell_boundaries folder

fovs

subset of fovs to use

z_indices

z indices of polygons to use

segm_to_use

segmentation results to use (usually = 1. Depends on if alternative segmentations were generated)

custom_polygon_names

a character vector to provide custom polygon names (optional)

flip_x_axis

flip x axis of polygon coordinates (multiply by -1)

flip_y_axis

flip y axis of polygon coordinates (multiply by -1)

calc_centroids

calculate centroids (default = FALSE)

smooth_polygons

smooth polygons (default = TRUE)

smooth_vertices

number of vertices for smoothing

set_neg_to_zero

set negative values to zero when smoothing

H5Fopen_flags

see H5Fopen for more details

cores

cores to use

create_gpoly_parallel

(default = TRUE) Whether to run gpoly creation in parallel

create_gpoly_bin

(Optional, default = FALSE) Parallelization option. Accepts integer values as an binning size when generating giottoPolygon objects

verbose

be verbose

output

whether to return as list of giottoPolygon or data.table

polygon_feat_types

deprecated. Use z_indices

Value

list of giottoPolygon or data.table

Details

Set H5Fopen_flags to "H5F_ACC_RDONLY" if you encounter permission issues.

See also

smoothGiottoPolygons