haystack: The main Haystack function

Description

The main Haystack function

Usage

haystack(x, ...)
# S3 method for matrix
haystack(
  x,
  dim1 = 1,
  dim2 = 2,
  detection,
  method = "highD",
  use.advanced.sampling = NULL,
  dir.randomization = NULL,
  scale = TRUE,
  grid.points = 100,
  grid.method = "centroid",
  ...
)
# S3 method for data.frame
haystack(
  x,
  dim1 = 1,
  dim2 = 2,
  detection,
  method = "highD",
  use.advanced.sampling = NULL,
  dir.randomization = NULL,
  scale = TRUE,
  grid.points = 100,
  grid.method = "centroid",
  ...
)
# S3 method for Seurat
haystack(
  x,
  assay = "RNA",
  slot = "data",
  coord = "pca",
  dims = NULL,
  cutoff = 1,
  method = NULL,
  use.advanced.sampling = NULL,
  ...
)
# S3 method for SingleCellExperiment
haystack(
  x,
  assay = "counts",
  coord = "TSNE",
  dims = NULL,
  cutoff = 1,
  method = NULL,
  use.advanced.sampling = NULL,
  ...
)

Value

An object of class "haystack"

Arguments

x: a matrix or other object from which coordinates of cells can be extracted.
...: further parameters passed down to methods.
dim1: column index or name of matrix for x-axis coordinates.
dim2: column index or name of matrix for y-axis coordinates.
detection: A logical matrix showing which genes (rows) are detected in which cells (columns)
method: choose between highD (default) and 2D haystack.
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.
scale: Logical (default=TRUE) indicating whether input coordinates in x should be scaled to mean 0 and standard deviation 1.
grid.points: An integer specifying the number of centers (gridpoints) to be used for estimating the density distributions of cells. Default is set to 100.
grid.method: The method to decide grid points for estimating the density in the high-dimensional space. Should be "centroid" (default) or "seeding".
assay: name of assay data for Seurat method.
slot: name of slot for assay data for Seurat method.
coord: name of coordinates slot for specific methods.
dims: dimensions from coord to use. By default, all.
cutoff: cutoff for detection.