overlapToMatrix

create a count matrix based on overlap results from calculateOverlap

Usage

# S4 method for giotto
overlapToMatrix(
  x,
  name = "raw",
  poly_info = NULL,
  feat_info = NULL,
  type = c("point", "intensity"),
  count_info_column = NULL,
  aggr_function = "sum",
  return_gobject = TRUE,
  verbose = TRUE,
  ...
)

# S4 method for giottoPolygon
overlapToMatrix(
  x,
  feat_info = "rna",
  type = c("point", "intensity"),
  count_info_column = NULL,
  output = c("Matrix", "data.table"),
  ...
)

# S4 method for SpatVector
overlapToMatrix(
  x,
  col_names = NULL,
  row_names = NULL,
  count_info_column = NULL,
  output = c("Matrix", "data.table"),
  verbose = TRUE,
  ...
)

# S4 method for data.table
overlapToMatrix(x, aggr_function = "sum", output = c("Matrix", "data.table"))

Arguments

x

object containing overlaps info. Can be giotto object or SpatVector points or data.table of overlaps generated from calculateOverlap

name

name for the overlap count matrix

poly_info

character. Polygon information to use

feat_info

character. Feature information to use

type

character. Type of overlap data (either 'point' or 'intensity')

count_info_column

column with count information

aggr_function

function to aggregate image information (default = sum)

return_gobject

return giotto object (default: TRUE)

verbose

be verbose

...

additional params to pass to methods

output

data format/class to return the results as

col_names, row_names

character vector. (optional) Set of row and col names that are expected to exist. This fixes the dimensions of the matrix since the overlaps information does not directly report rows and cols where no values were detected.

Value

giotto object or count matrix