readPolygonFilesVizgenHDF5_old: 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_old(
  boundaries_path,
  fovs = NULL,
  polygon_feat_types = 0:6,
  custom_polygon_names = NULL,
  flip_x_axis = F,
  flip_y_axis = F,
  smooth_polygons = TRUE,
  smooth_vertices = 60,
  set_neg_to_zero = FALSE,
  H5Fopen_flags = "H5F_ACC_RDWR",
  cores = NA,
  verbose = TRUE
)

Arguments

boundaries_path	path to the cell_boundaries folder
fovs	subset of fovs to use
polygon_feat_types	a vector containing the polygon feature types
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)
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
verbose	be verbose

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.