readPolygonFilesVizgenHDF5

Source: R/general_help.R

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

readPolygonFilesVizgenHDF5_old(
  boundaries_path,
  fovs = NULL,
  polygon_feat_types = 0:6,
  custom_polygon_names = NULL,
  flip_x_axis = FALSE,
  flip_y_axis = FALSE,
  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

Value

data.table

Details

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