The main Haystack function, for 2-dimensional spaces.

The main Haystack function, for 2-dimensional spaces.

haystack_2D(
  x,
  y,
  detection,
  use.advanced.sampling = NULL,
  dir.randomization = NULL
)

Arguments

x

x-axis coordinates of cells in a 2D representation (e.g. resulting from PCA or t-SNE)

y

y-axis coordinates of cells in a 2D representation

detection

A logical matrix showing which genes (rows) are detected in which cells (columns)

use.advanced.sampling

If NULL naive sampling is used. If a vector is given (of length = no. of cells) sampling is done according to the values in the vector.

dir.randomization

If NULL, no output is made about the random sampling step. If not NULL, files related to the randomizations are printed to this directory.

Value

An object of class "haystack"