readPolygonFilesVizgenHDF5#
Last Updated: Oct 02, 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#
|
path to the cell_boundaries folder |
|
subset of fovs to use |
|
a vector containing the polygon feature types |
|
a character vector to provide custom polygon names (optional) |
|
flip x axis of polygon coordinates (multiply by -1) |
|
flip y axis of polygon coordinates (multiply by -1) |
|
smooth polygons (default = TRUE) |
|
number of vertices for smoothing |
|
set negative values to zero when smoothing |
|
see |
|
be verbose |
Details#
Set H5Fopen_flags to “H5F_ACC_RDONLY” if you encounter permission issues.
See Also#
smoothGiottoPolygons