Description Usage Arguments Details Value Author(s) Examples

Calculate pairwise distance from a matrix

1 |

`mat` |
a matrix. The distance is calculated by rows. |

`pairwise_fun` |
a function which calculates distance between two vectors. |

`...` |
pass to |

You can construct any type of distance measurements by defining a pair-wise distance function.
The function is implemented by two nested `for`

loops, so the efficiency may not be so good.

A `dist`

object.

Zuguang Gu <[email protected]>

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
mat = matrix(rnorm(40), nr = 4, ncol = 10)
rownames(mat) = letters[1:4]
colnames(mat) = letters[1:10]
d2 = dist2(mat)
d2 = dist2(mat, pairwise_fun = function(x, y) 1 - cor(x, y))
# distance only calculated within 10 and 90 quantile of each vector
d2 = dist2(mat, pairwise_fun = function(x, y) {
q1 = quantile(x, c(0.1, 0.9))
q2 = quantile(y, c(0.1, 0.9))
l = x > q1[1] & x < q1[2] & y > q2[1] & y < q2[2]
sqrt(sum((x[l] - y[l])^2))
})
``` |

eilslabs/ComplexHeatmap documentation built on Oct. 19, 2017, 2:13 p.m.

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