singleCellHaystack (version 0.3.4)

haystack_2D: The main Haystack function, for 2-dimensional spaces.

Description

The main Haystack function, for 2-dimensional spaces.

Usage

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

Value

An object of class "haystack"

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.

Examples

# using the toy example of the singleCellHaystack package
# define a logical matrix with detection of each gene (rows) in each cell (columns)
dat.detection <- dat.expression > 1

# running haystack in default mode
res <- haystack(dat.tsne, detection=dat.detection, method = "2D")
# list top 10 biased genes
show_result_haystack(res, n =10)