readPolygonFilesVizgenHDF5: readPolygonFilesVizgenHDF5

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

readPolygonFilesVizgenHDF5

Description

Read and create polygons for all cells, or for only selected FOVs.

Usage

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 = NA,
  create_gpoly_parallel = TRUE,
  create_gpoly_bin = FALSE,
  verbose = TRUE,
  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
polygon_feat_types	deprecated. Use z_indices

Details

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

See Also

smoothGiottoPolygons

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