Description Usage Arguments Value

Establish rough neighbor matching between samples given their projections in a common space

1 2 3 4 5 6 7 8 9 10 11 | ```
getNeighborMatrix(
p1,
p2,
k,
k1 = k,
matching = "mNN",
metric = "angular",
l2.sigma = 1e+05,
cor.base = 1,
min.similarity = 1e-05
)
``` |

`p1` |
projection of sample 1 |

`p2` |
projection of sample 2 |

`k` |
neighborhood radius |

`k1` |
neighborhood radius |

`matching` |
string mNN (default) or NN (default='mNN') |

`metric` |
string Distance type (default: "angular", can also be 'L2') |

`l2.sigma` |
numeric L2 distances get transformed as exp(-d/sigma) using this value (default=1e5) |

`cor.base` |
numeric (default=1) |

`min.similarity` |
minimal similarity between two cells, required to have an edge |

matrix with the similarity (!) values corresponding to weight (1-d for angular, and exp(-d/l2.sigma) for L2)

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