RDocumentation: corrplot

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if(!require('corrplot')) {
    install.packages('corrplot')
    library('corrplot')
}

data(mtcars)
M = cor(mtcars)
set.seed(0)

##  different color series
## COL2: Get diverging colors
## c('RdBu', 'BrBG', 'PiYG', 'PRGn', 'PuOr', 'RdYlBu')
## COL1: Get sequential colors
## c('Oranges', 'Purples', 'Reds', 'Blues', 'Greens', 'Greys', 'OrRd', 'YlOrRd', 'YlOrBr', 'YlGn')

wb = c('white', 'black')

par(ask = TRUE)

## different color scale and methods to display corr-matrix
corrplot(M, method = 'number', col = 'black', cl.pos = 'n')
corrplot(M, method = 'number')
corrplot(M)
corrplot(M, order = 'AOE')
corrplot(M, order = 'AOE', addCoef.col = 'grey')

corrplot(M, order = 'AOE',  cl.length = 21, addCoef.col = 'grey')
corrplot(M, order = 'AOE', col = COL2(n=10), addCoef.col = 'grey')

corrplot(M, order = 'AOE', col = COL2('PiYG'))
corrplot(M, order = 'AOE', col = COL2('PRGn'), addCoef.col = 'grey')
corrplot(M, order = 'AOE', col = COL2('PuOr', 20), cl.length = 21, addCoef.col = 'grey')
corrplot(M, order = 'AOE', col = COL2('PuOr', 10), addCoef.col = 'grey')

corrplot(M, order = 'AOE', col = COL2('RdYlBu', 100))
corrplot(M, order = 'AOE', col = COL2('RdYlBu', 10))


corrplot(M, method = 'color', col = COL2(n=20), cl.length = 21, order = 'AOE',
         addCoef.col = 'grey')
corrplot(M, method = 'square', col = COL2(n=200), order = 'AOE')
corrplot(M, method = 'ellipse', col = COL2(n=200), order = 'AOE')
corrplot(M, method = 'shade', col = COL2(n=20), order = 'AOE')
corrplot(M, method = 'pie', order = 'AOE')

## col = wb
corrplot(M, col = wb, order = 'AOE', outline = TRUE, cl.pos = 'n')

## like Chinese wiqi, suit for either on screen or white-black print.
corrplot(M, col = wb, bg = 'gold2',  order = 'AOE', cl.pos = 'n')


## mixed methods: It's more efficient if using function 'corrplot.mixed'
## circle + ellipse
corrplot(M, order = 'AOE', type = 'upper', tl.pos = 'd')
corrplot(M, add = TRUE, type = 'lower', method = 'ellipse', order = 'AOE',
         diag = FALSE, tl.pos = 'n', cl.pos = 'n')

## circle + square
corrplot(M, order = 'AOE', type = 'upper', tl.pos = 'd')
corrplot(M, add = TRUE, type = 'lower', method = 'square', order = 'AOE',
         diag = FALSE, tl.pos = 'n', cl.pos = 'n')

## circle + colorful number
corrplot(M, order = 'AOE', type = 'upper', tl.pos = 'd')
corrplot(M, add = TRUE, type = 'lower', method = 'number', order = 'AOE',
         diag = FALSE, tl.pos = 'n', cl.pos = 'n')

## circle + black number
corrplot(M, order = 'AOE', type = 'upper', tl.pos = 'tp')
corrplot(M, add = TRUE, type = 'lower', method = 'number', order = 'AOE',
         col = 'black', diag = FALSE, tl.pos = 'n', cl.pos = 'n')


## order is hclust and draw rectangles
corrplot(M, order = 'hclust')
corrplot(M, order = 'hclust', addrect = 2)
corrplot(M, order = 'hclust', addrect = 3, rect.col = 'red')
corrplot(M, order = 'hclust', addrect = 4, rect.col = 'blue')
corrplot(M, order = 'hclust', hclust.method = 'ward.D2', addrect = 4)

## visualize a  matrix in [0, 1]
corrplot(abs(M), order = 'AOE', col.lim = c(0, 1))
corrplot(abs(M), order = 'AOE', is.corr = FALSE,  col.lim = c(0, 1))


# when is.corr=TRUE, col.lim only affect the color legend
# If you change it, the color is still assigned on [-1, 1]
corrplot(M/2)
corrplot(M/2, col.lim = c(-0.5, 0.5))

# when is.corr=FALSE, col.lim is also used to assign colors
# if the matrix have both positive and negative values
# the matrix transformation keep every values positive and negative
corrplot(M*2, is.corr = FALSE, col.lim = c(-2, 2))
corrplot(M*2, is.corr = FALSE, col.lim = c(-2, 2) * 2)
corrplot(M*2, is.corr = FALSE, col.lim = c(-2, 2) * 4)

## 0.5~0.6
corrplot(abs(M)/10+0.5, col = COL1('Greens', 10))
corrplot(abs(M)/10+0.5, is.corr = FALSE, col.lim = c(0.5, 0.6), col = COL1('YlGn', 10))


## visualize a  matrix in [-100, 100]
ran = round(matrix(runif(225, -100, 100), 15))
corrplot(ran, is.corr = FALSE)
corrplot(ran, is.corr = FALSE, col.lim = c(-100, 100))

## visualize a matrix in [100, 300]
ran2 = ran + 200

# bad color, not suitable for a matrix in [100, 300]
corrplot(ran2, is.corr = FALSE, col.lim = c(100, 300), col = COL2(, 100))

# good color
corrplot(ran2, is.corr = FALSE, col.lim = c(100, 300), col = COL1(, 100))


## text-labels and plot type
corrplot(M, order = 'AOE', tl.srt = 45)
corrplot(M, order = 'AOE', tl.srt = 60)
corrplot(M, order = 'AOE', tl.pos = 'd', cl.pos = 'n')
corrplot(M, order = 'AOE', diag = FALSE, tl.pos = 'd')
corrplot(M, order = 'AOE', type = 'upper')
corrplot(M, order = 'AOE', type = 'upper', diag = FALSE)
corrplot(M, order = 'AOE', type = 'lower', cl.pos = 'b')
corrplot(M, order = 'AOE', type = 'lower', cl.pos = 'b', diag = FALSE)



#### color-legend
corrplot(M, order = 'AOE', cl.ratio = 0.2, cl.align = 'l')
corrplot(M, order = 'AOE', cl.ratio = 0.2, cl.align = 'c')
corrplot(M, order = 'AOE', cl.ratio = 0.2, cl.align = 'r')
corrplot(M, order = 'AOE', cl.pos = 'b')
corrplot(M, order = 'AOE', cl.pos = 'b', tl.pos = 'd')
corrplot(M, order = 'AOE', cl.pos = 'n')


## deal with missing Values
M2 = M
diag(M2) = NA
corrplot(M2)
corrplot(M2, na.label = 'o')
corrplot(M2, na.label = 'NA')


##the input matrix is not square
corrplot(M[1:8, ])
corrplot(M[, 1:8])

testRes = cor.mtest(mtcars, conf.level = 0.95)

## specialized the insignificant value according to the significant level
corrplot(M, p.mat = testRes$p, sig.level = 0.05, order = 'hclust', addrect = 2)

## leave blank on no significant coefficient
corrplot(M, p.mat = testRes$p, method = 'circle', type = 'lower', insig ='blank',
         addCoef.col ='black', number.cex = 0.8, order = 'AOE', diag = FALSE)

## add p-values on no significant coefficients
corrplot(M, p.mat = testRes$p, insig = 'p-value')

## add all p-values
corrplot(M, p.mat = testRes$p, insig = 'p-value', sig.level = -1)

## add significant level stars
corrplot(M, p.mat = testRes$p, method = 'color', diag = FALSE, type = 'upper',
         sig.level = c(0.001, 0.01, 0.05), pch.cex = 0.9,
         insig = 'label_sig', pch.col = 'grey20', order = 'AOE')

## add significant level stars and cluster rectangles
corrplot(M, p.mat = testRes$p, tl.pos = 'd', order = 'hclust', addrect = 2,
         insig = 'label_sig', sig.level = c(0.001, 0.01, 0.05),
         pch.cex = 0.9, pch.col = 'grey20')

# Visualize confidence interval
corrplot(M, lowCI = testRes$lowCI, uppCI = testRes$uppCI, order = 'hclust',
         tl.pos = 'd', rect.col = 'navy', plotC = 'rect', cl.pos = 'n')

# Visualize confidence interval and cross the significant coefficients
corrplot(M, p.mat = testRes$p, lowCI = testRes$lowCI, uppCI = testRes$uppCI,
         addrect = 3, rect.col = 'navy', plotC = 'rect', cl.pos = 'n')



res1 = cor.mtest(mtcars, conf.level = 0.95)
res2 = cor.mtest(mtcars, conf.level = 0.99)


## plot confidence interval(0.95), 'circle' method
corrplot(M, low = res1$uppCI, upp = res1$uppCI,
         plotCI = 'circle', addg = 'grey20', cl.pos = 'n')
corrplot(M, p.mat = res1$p, low = res1$lowCI, upp = res1$uppCI,
         plotCI = 'circle', addg = 'grey20', cl.pos = 'n')
corrplot(M, low = res1$lowCI, upp = res1$uppCI,
         col = c('white', 'black'), bg = 'gold2', order = 'AOE',
         plotCI = 'circle', cl.pos = 'n', pch.col = 'red')
corrplot(M, p.mat = res1$p, low = res1$lowCI, upp = res1$uppCI,
         col = c('white', 'black'), bg = 'gold2', order = 'AOE',
         plotCI = 'circle', cl.pos = 'n', pch.col = 'red')

## plot confidence interval(0.95), 'square' method
corrplot(M, low = res1$lowCI, upp = res1$uppCI,
         col = c('white', 'black'), bg = 'gold2', order = 'AOE',
         plotCI = 'square', addg = NULL, cl.pos = 'n')
corrplot(M, p.mat = res1$p, low = res1$lowCI, upp = res1$uppCI,
         col = c('white', 'black'), bg = 'gold2', order = 'AOE', pch.col = 'red',
         plotCI = 'square', addg = NULL, cl.pos = 'n')

## plot confidence interval0.95, 0.95, 0.99, 'rect' method
corrplot(M, low = res1$lowCI, upp = res1$uppCI, order = 'hclust',
         rect.col = 'navy', plotCI = 'rect', cl.pos = 'n')
corrplot(M, p.mat = res1$p, low = res1$lowCI, upp = res1$uppCI,
         order = 'hclust', pch.col = 'red', sig.level = 0.05, addrect = 3,
         rect.col = 'navy', plotCI = 'rect', cl.pos = 'n')
corrplot(M, p.mat = res2$p, low = res2$lowCI, upp = res2$uppCI,
         order = 'hclust', pch.col = 'red', sig.level = 0.01, addrect = 3,
         rect.col = 'navy', plotCI = 'rect', cl.pos = 'n')


## an animation of changing confidence interval in different significance level
## begin.animaton
par(ask = FALSE)
for (i in seq(0.1, 0, -0.005)) {
  tmp = cor.mtest(mtcars, conf.level = 1 - i)
  corrplot(M, p.mat = tmp$p, low = tmp$lowCI, upp = tmp$uppCI, order = 'hclust',
           pch.col = 'red', sig.level = i, plotCI = 'rect', cl.pos = 'n',
           mar = c(0, 0, 1, 0),
           title = substitute(alpha == x,
                              list(x = format(i, digits = 3, nsmall = 3))))
  Sys.sleep(0.15)
}
## end.animaton