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", "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 = tan (e_{i2}/e_{i1}), if e_{i1}>0

    a_i = tan (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", "single", "complete", "average", "mcquitty", "median" or "centroid".

Value

Returns a single permutation vector.

Author(s)

Taiyun Wei

See Also

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"))
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]



par(ask=TRUE)
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")
[Package corrplot version 0.73 Index]