corrMatOrder {corrplot} R Documentation

## Reorder a correlation matrix.

### Description

Draw rectangle(s) around the chart of corrrlation matrix based on the number of each cluster's members.

### Usage

```corrMatOrder(
corr,
order = c("AOE", "FPC", "hclust", "alphabet"),
hclust.method = c("complete", "ward", "ward.D", "ward.D2", "single", "average",
"mcquitty", "median", "centroid")
)
```

### Arguments

 `corr` Correlation matrix to reorder. `order` Character, the ordering method for the correlation matrix. `'AOE'` for the angular order of the eigenvectors. It is calculated from the order of the angles, a_i: a_i = arctan (e_{i2} / e_{i1}), if e_{i1} > 0 a_i = arctan (e_{i2} / e_{i1}) + π, otherwise. where e_1 and e_2 are the largest two eigenvalues of matrix `corr`. See Michael Friendly (2002) for details. `'FPC'` for the first principal component order. `'hclust'` for hierarchical clustering order. `'alphabet'` for alphabetical order. `hclust.method` Character, the agglomeration method to be used when `order` is `hclust`. This should be one of `'ward'`, `'ward.D'`, `'ward.D2'`, `'single'`, `'complete'`, `'average'`, `'mcquitty'`, `'median'` or `'centroid'`.

### Value

Returns a single permutation vector.

### Author(s)

Taiyun Wei

Package `seriation` offers more methods to reorder matrices, such as ARSA, BBURCG, BBWRCG, MDS, TSP, Chen and so forth.

### Examples

```M = cor(mtcars)

(order.AOE = corrMatOrder(M, order = 'AOE'))
(order.FPC = corrMatOrder(M, order = 'FPC'))
(order.hc = corrMatOrder(M, order = 'hclust'))
(order.hc2 = corrMatOrder(M, order = 'hclust', hclust.method = 'ward.D'))

M.AOE = M[order.AOE,order.AOE]
M.FPC = M[order.FPC,order.FPC]
M.hc  = M[order.hc, order.hc]
M.hc2 = M[order.hc2,order.hc2]

corrplot(M)
corrplot(M.AOE)
corrplot(M.FPC)
corrplot(M.hc)

corrplot(M.hc)
corrRect.hclust(corr = M.hc, k = 2)

corrplot(M.hc)
corrRect.hclust(corr = M.hc, k = 3)

corrplot(M.hc2)
corrRect.hclust(M.hc2, k = 2, method = 'ward.D')
```

[Package corrplot version 0.90 Index]