Description Usage Arguments Value Examples

View source: R/haystack_highD.R

The main Haystack function, for higher-dimensional spaces.

1 2 3 4 5 6 7 8 9 | ```
haystack_highD(
x,
detection,
grid.points = 100,
use.advanced.sampling = NULL,
dir.randomization = NULL,
scale = TRUE,
grid.method = "centroid"
)
``` |

`x` |
Coordinates of cells in a 2D or higher-dimensional space. Rows represent cells, columns the dimensions of the space. |

`detection` |
A logical matrix showing which genes (rows) are detected in which cells (columns) |

`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. |

`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.method` |
The method to decide grid points for estimating the density in the high-dimensional space. Should be "centroid" (default) or "seeding". |

An object of class "haystack", including the results of the analysis, and the coordinates of the grid points used to estimate densities.

1 2 | ```
# I need to add some examples.
# A toy example will be added too.
``` |

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