kinship.heatmap {ASRgenomics} | R Documentation |

## Enhanced heatmap plot for a kinship matrix K

### Description

Generates a heatmap with dendrogram based on a provided kinship matrix.
This matrix can be a pedigree relationship matrix `\boldsymbol{A}`

, a
genomic relationship matrix `\boldsymbol{G}`

or a hybrid relationship
matrix `\boldsymbol{H}`

.
Individual names should be assigned to `rownames`

and `colnames`

.
It sorts individuals according to dendrogram in both columns and rows.

### Usage

```
kinship.heatmap(
K = NULL,
dendrogram = TRUE,
clustering.method = c("hierarchical", "kmeans"),
dist.method = c("euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski"),
row.label = TRUE,
col.label = FALSE
)
```

### Arguments

`K` |
Input of a kinship matrix in full format ( |

`dendrogram` |
If |

`clustering.method` |
The clustering method considered for the dendrogram.
Options are: |

`dist.method` |
The method considered to calculate the distance matrix between
individuals used for hierarchical clustering. Options are: |

`row.label` |
If |

`col.label` |
If |

### Details

Uses the library `superheat`

from Barter and Yu (2018) to generate plots.

### Value

A plot with the properties specified by the above arguments.

### References

Barter, R.L. and Yu, B. 2018. Superheat: An R package for creating beautiful and extendable heatmaps for visualizing complex data. J. Comput. Graph. Stat. 27(4):910-922.

### Examples

```
# Get G matrix.
G <- G.matrix(M = geno.apple, method = "VanRaden")$G
G[1:5, 1:5]
# Plot a subset of the individuals.
kinship.heatmap(K = G[1:10, 1:10], dendrogram = TRUE, row.label = TRUE, col.label = TRUE)
```

*ASRgenomics*version 1.1.4 Index]