Sort a correlation matrix to improve readability of groups and clusters
Source:R/cor_sort.R
cor_sort.RdSort a correlation matrix based on hclust().
Arguments
- x
A correlation matrix.
- distance
How the distance between each variable should be calculated. If
correlation(default; suited for correlation matrices), the matrix will be rescaled to 0-1 (distance = 0indicating correlation of1;distance = 1indicating correlation of-1). Ifraw, then the matrix will be used as a distance matrix as-is. Can be others (euclidean,manhattan, ...), in which case it will be passed todist()(see the arguments for it).- hclust_method
Argument passed down into the
methodargument ofhclust().- ...
Other arguments to be passed to or from other functions.
Examples
x <- correlation(mtcars)
cor_sort(as.matrix(x))
#> carb wt hp cyl disp qsec
#> carb 1.00000000 0.4276059 0.7498125 0.5269883 0.3949769 -0.65624923
#> wt 0.42760594 1.0000000 0.6587479 0.7824958 0.8879799 -0.17471588
#> hp 0.74981247 0.6587479 1.0000000 0.8324475 0.7909486 -0.70822339
#> cyl 0.52698829 0.7824958 0.8324475 1.0000000 0.9020329 -0.59124207
#> disp 0.39497686 0.8879799 0.7909486 0.9020329 1.0000000 -0.43369788
#> qsec -0.65624923 -0.1747159 -0.7082234 -0.5912421 -0.4336979 1.00000000
#> vs -0.56960714 -0.5549157 -0.7230967 -0.8108118 -0.7104159 0.74453544
#> mpg -0.55092507 -0.8676594 -0.7761684 -0.8521620 -0.8475514 0.41868403
#> drat -0.09078980 -0.7124406 -0.4487591 -0.6999381 -0.7102139 0.09120476
#> am 0.05753435 -0.6924953 -0.2432043 -0.5226070 -0.5912270 -0.22986086
#> gear 0.27407284 -0.5832870 -0.1257043 -0.4926866 -0.5555692 -0.21268223
#> vs mpg drat am gear
#> carb -0.5696071 -0.5509251 -0.09078980 0.05753435 0.2740728
#> wt -0.5549157 -0.8676594 -0.71244065 -0.69249526 -0.5832870
#> hp -0.7230967 -0.7761684 -0.44875912 -0.24320426 -0.1257043
#> cyl -0.8108118 -0.8521620 -0.69993811 -0.52260705 -0.4926866
#> disp -0.7104159 -0.8475514 -0.71021393 -0.59122704 -0.5555692
#> qsec 0.7445354 0.4186840 0.09120476 -0.22986086 -0.2126822
#> vs 1.0000000 0.6640389 0.44027846 0.16834512 0.2060233
#> mpg 0.6640389 1.0000000 0.68117191 0.59983243 0.4802848
#> drat 0.4402785 0.6811719 1.00000000 0.71271113 0.6996101
#> am 0.1683451 0.5998324 0.71271113 1.00000000 0.7940588
#> gear 0.2060233 0.4802848 0.69961013 0.79405876 1.0000000
cor_sort(x, hclust_method = "ward.D2") # It can also reorder the long form output
#> # Correlation Matrix (pearson-method)
#>
#> Parameter1 | Parameter2 | r | 95% CI | t(30) | p
#> --------------------------------------------------------------------
#> wt | carb | 0.43 | [ 0.09, 0.68] | 2.59 | 0.205
#> wt | qsec | -0.17 | [-0.49, 0.19] | -0.97 | > .999
#> wt | vs | -0.55 | [-0.76, -0.26] | -3.65 | 0.023*
#> wt | am | -0.69 | [-0.84, -0.45] | -5.26 | < .001***
#> wt | gear | -0.58 | [-0.77, -0.29] | -3.93 | 0.012*
#> cyl | wt | 0.78 | [ 0.60, 0.89] | 6.88 | < .001***
#> cyl | disp | 0.90 | [ 0.81, 0.95] | 11.45 | < .001***
#> cyl | hp | 0.83 | [ 0.68, 0.92] | 8.23 | < .001***
#> cyl | carb | 0.53 | [ 0.22, 0.74] | 3.40 | 0.041*
#> cyl | qsec | -0.59 | [-0.78, -0.31] | -4.02 | 0.010*
#> cyl | vs | -0.81 | [-0.90, -0.64] | -7.59 | < .001***
#> cyl | drat | -0.70 | [-0.84, -0.46] | -5.37 | < .001***
#> cyl | am | -0.52 | [-0.74, -0.21] | -3.36 | 0.043*
#> cyl | gear | -0.49 | [-0.72, -0.17] | -3.10 | 0.079
#> disp | wt | 0.89 | [ 0.78, 0.94] | 10.58 | < .001***
#> disp | hp | 0.79 | [ 0.61, 0.89] | 7.08 | < .001***
#> disp | carb | 0.39 | [ 0.05, 0.65] | 2.35 | 0.303
#> disp | qsec | -0.43 | [-0.68, -0.10] | -2.64 | 0.197
#> disp | vs | -0.71 | [-0.85, -0.48] | -5.53 | < .001***
#> disp | drat | -0.71 | [-0.85, -0.48] | -5.53 | < .001***
#> disp | am | -0.59 | [-0.78, -0.31] | -4.02 | 0.010*
#> disp | gear | -0.56 | [-0.76, -0.26] | -3.66 | 0.023*
#> hp | wt | 0.66 | [ 0.40, 0.82] | 4.80 | 0.001**
#> hp | carb | 0.75 | [ 0.54, 0.87] | 6.21 | < .001***
#> hp | qsec | -0.71 | [-0.85, -0.48] | -5.49 | < .001***
#> hp | vs | -0.72 | [-0.86, -0.50] | -5.73 | < .001***
#> hp | drat | -0.45 | [-0.69, -0.12] | -2.75 | 0.170
#> hp | am | -0.24 | [-0.55, 0.12] | -1.37 | > .999
#> hp | gear | -0.13 | [-0.45, 0.23] | -0.69 | > .999
#> qsec | carb | -0.66 | [-0.82, -0.40] | -4.76 | 0.001**
#> qsec | vs | 0.74 | [ 0.53, 0.87] | 6.11 | < .001***
#> qsec | am | -0.23 | [-0.54, 0.13] | -1.29 | > .999
#> qsec | gear | -0.21 | [-0.52, 0.15] | -1.19 | > .999
#> vs | carb | -0.57 | [-0.77, -0.28] | -3.80 | 0.017*
#> vs | am | 0.17 | [-0.19, 0.49] | 0.94 | > .999
#> vs | gear | 0.21 | [-0.15, 0.52] | 1.15 | > .999
#> mpg | wt | -0.87 | [-0.93, -0.74] | -9.56 | < .001***
#> mpg | cyl | -0.85 | [-0.93, -0.72] | -8.92 | < .001***
#> mpg | disp | -0.85 | [-0.92, -0.71] | -8.75 | < .001***
#> mpg | hp | -0.78 | [-0.89, -0.59] | -6.74 | < .001***
#> mpg | carb | -0.55 | [-0.75, -0.25] | -3.62 | 0.024*
#> mpg | qsec | 0.42 | [ 0.08, 0.67] | 2.53 | 0.222
#> mpg | vs | 0.66 | [ 0.41, 0.82] | 4.86 | 0.001**
#> mpg | drat | 0.68 | [ 0.44, 0.83] | 5.10 | < .001***
#> mpg | am | 0.60 | [ 0.32, 0.78] | 4.11 | 0.008**
#> mpg | gear | 0.48 | [ 0.16, 0.71] | 3.00 | 0.097
#> drat | wt | -0.71 | [-0.85, -0.48] | -5.56 | < .001***
#> drat | carb | -0.09 | [-0.43, 0.27] | -0.50 | > .999
#> drat | qsec | 0.09 | [-0.27, 0.43] | 0.50 | > .999
#> drat | vs | 0.44 | [ 0.11, 0.68] | 2.69 | 0.187
#> drat | am | 0.71 | [ 0.48, 0.85] | 5.57 | < .001***
#> drat | gear | 0.70 | [ 0.46, 0.84] | 5.36 | < .001***
#> am | carb | 0.06 | [-0.30, 0.40] | 0.32 | > .999
#> am | gear | 0.79 | [ 0.62, 0.89] | 7.16 | < .001***
#> gear | carb | 0.27 | [-0.08, 0.57] | 1.56 | > .999
#>
#> p-value adjustment method: Holm (1979)
#> Observations: 32
cor_sort(summary(x, redundant = TRUE)) # As well as from the summary
#> # Correlation Matrix (pearson-method)
#>
#> Parameter | carb | wt | hp | cyl | disp | qsec
#> ---------------------------------------------------------------------------
#> carb | | 0.43*** | 0.75*** | 0.53*** | 0.39*** | -0.66***
#> wt | 0.43*** | | 0.66*** | 0.78*** | 0.89*** | -0.17***
#> hp | 0.75*** | 0.66*** | | 0.83*** | 0.79*** | -0.71***
#> cyl | 0.53*** | 0.78*** | 0.83*** | | 0.90 | -0.59**
#> disp | 0.39*** | 0.89*** | 0.79*** | 0.90 | | -0.43***
#> qsec | -0.66*** | -0.17*** | -0.71*** | -0.59** | -0.43*** |
#> vs | -0.57 | -0.55* | -0.72 | -0.81*** | -0.71 | 0.74
#> mpg | -0.55** | -0.87*** | -0.78*** | -0.85*** | -0.85 | 0.42*
#> drat | -0.09** | -0.71* | -0.45* | -0.70 | -0.71*** | 0.09***
#> am | 0.06 | -0.69 | -0.24* | -0.52 | -0.59*** | -0.23*
#> gear | 0.27* | -0.58* | -0.13 | -0.49*** | -0.56 | -0.21
#>
#> Parameter | vs | mpg | drat | am | gear
#> ----------------------------------------------------------------
#> carb | -0.57 | -0.55** | -0.09** | 0.06 | 0.27*
#> wt | -0.55* | -0.87*** | -0.71* | -0.69 | -0.58*
#> hp | -0.72 | -0.78*** | -0.45* | -0.24* | -0.13
#> cyl | -0.81*** | -0.85*** | -0.70 | -0.52 | -0.49***
#> disp | -0.71 | -0.85 | -0.71*** | -0.59*** | -0.56
#> qsec | 0.74 | 0.42* | 0.09*** | -0.23* | -0.21
#> vs | | 0.66*** | 0.44 | 0.17 | 0.21**
#> mpg | 0.66*** | | 0.68 | 0.60 | 0.48*
#> drat | 0.44 | 0.68 | | 0.71*** | 0.70
#> am | 0.17 | 0.60 | 0.71*** | | 0.79
#> gear | 0.21** | 0.48* | 0.70 | 0.79 |
#>
#> p-value adjustment method: Holm (1979)