haystack_2D function

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.

Returns

An object of class "haystack"