readPolygonFilesVizgenHDF5#

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Last Updated: Mar 11, 2023

Description#

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

Usage#

readPolygonFilesVizgenHDF5(
  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",
  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
`verbose`	be verbose

Details#

Set H5Fopen_flags to “H5F_ACC_RDONLY” if you encounter permission issues.

See Also#

smoothGiottoPolygons