readPolygonFilesVizgen

Source: R/general_help.R

Read selected polygon files for the FOVs present in the Giotto object and add the smoothed polygons to the object

readPolygonFilesVizgen(
  gobject,
  boundaries_path,
  fovs = NULL,
  polygon_feat_types = 0:6,
  flip_x_axis = FALSE,
  flip_y_axis = FALSE,
  smooth_polygons = TRUE,
  smooth_vertices = 60,
  set_neg_to_zero = FALSE,
  return_gobject = TRUE,
  verbose = TRUE
)

.h5_read_vizgen(
  h5File,
  z_indices = 1L:7L,
  segm_to_use = "p_0",
  H5Fopen_flags = "H5F_ACC_RDWR"
)

Arguments

gobject

giotto object

boundaries_path

path to the cell_boundaries folder

fovs

selected fovs, if NULL select all fovs within Giotto object

polygon_feat_types

a vector containing the polygon feature types

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

return_gobject

return giotto object

verbose

be verbose

Value

giotto object or cell polygons list

Functions

  • .h5_read_vizgen(): (internal) Optimized .hdf5 reading for vizgen merscope output. Returns a data.table of xyz coords and cell_id