haystack function

The main Haystack function

haystack(x, ...)

## S3 method for class 'matrix'
haystack(
  x,
  expression,
  weights.advanced.Q = NULL,
  dir.randomization = NULL,
  scale = TRUE,
  grid.points = 100,
  grid.method = "centroid",
  ...
)

## S3 method for class 'data.frame'
haystack(
  x,
  expression,
  weights.advanced.Q = NULL,
  dir.randomization = NULL,
  scale = TRUE,
  grid.points = 100,
  grid.method = "centroid",
  ...
)

## S3 method for class 'Seurat'
haystack(
  x,
  coord,
  assay = "RNA",
  slot = "data",
  dims = NULL,
  cutoff = 1,
  method = NULL,
  weights.advanced.Q = NULL,
  ...
)

## S3 method for class 'SingleCellExperiment'
haystack(
  x,
  assay = "counts",
  coord = "TSNE",
  dims = NULL,
  cutoff = 1,
  method = NULL,
  weights.advanced.Q = NULL,
  ...
)

Arguments

• x: a matrix or other object from which coordinates of cells can be extracted.
• ...: further parameters passed down to methods.
• expression: a matrix with expression data of genes (rows) in cells (columns)
• weights.advanced.Q: 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".
• coord: name of coordinates slot for specific methods.
• assay: name of assay data for Seurat method.
• slot: name of slot for assay data for Seurat method.
• dims: dimensions from coord to use. By default, all.
• cutoff: cutoff for detection.
• method: choose between highD (default) and 2D haystack.

Returns

An object of class "haystack"