haystack {singleCellHaystack}

The main Haystack function

Description

The main Haystack function

Usage

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.

Value

An object of class "haystack"