subsetGiottoLocs: subsetGiottoLocs

In bernard2012/Giotto: Spatial single-cell transcriptomics toolbox

Description

subsets Giotto object based on spatial locations

Usage

subsetGiottoLocs(
  gobject,
  x_max = NULL,
  x_min = NULL,
  y_max = NULL,
  y_min = NULL,
  z_max = NULL,
  z_min = NULL,
  return_gobject = T,
  verbose = FALSE
)

Arguments

gobject	giotto object
x_max	maximum x-coordinate
x_min	minimum x-coordinate
y_max	maximum y-coordinate
y_min	minimum y-coordinate
z_max	maximum z-coordinate
z_min	minimum z-coordinate
return_gobject	return Giotto object
verbose	be verbose

Details

if return_gobject = FALSE, then a filtered combined metadata data.table will be returned

Value

giotto object

Examples

data(mini_giotto_single_cell)

# spatial plot
spatPlot(mini_giotto_single_cell)

# subset giotto object based on spatial locations
subset_obj = subsetGiottoLocs(mini_giotto_single_cell,
x_max = 1500, x_min = 1000,
y_max = -500, y_min = -1000)

# spatial plot of subset giotto object
spatPlot(subset_obj)

bernard2012/Giotto documentation built on Sept. 22, 2020, 10:29 a.m.