readPolygonFilesVizgen: readPolygonFilesVizgen

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

readPolygonFilesVizgen

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
)

h5read_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

Functions

• h5read_vizgen(): (internal) Optimized .hdf5 reading for vizgen merscope output. Returns a data.table of xyz coords and cell_id

See Also

smoothGiottoPolygons

drieslab/Giotto_site_suite documentation built on April 26, 2023, 11:51 p.m.