readPolygonFilesVizgen#

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Last Updated: Mar 11, 2023

Description#

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

Usage#

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

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

See Also#

smoothGiottoPolygons