readPolygonFilesVizgen#

Date

2022-10-06

https://github.com/drieslab/Giotto/tree/suite/R/general_help.R#L1446

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#

Argument

Description

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

Seealso#

smoothGiottoPolygons