tests/testthat/test-corrplot.R

In corrplot: Visualization of a Correlation Matrix

context('Visualization of a correlation matrix')

# Tests ==========

test_that('Testing `cl.pos` parameter', {
  M = cor(mtcars)
  expect_silent(corrplot(M, cl.pos = TRUE, diag = FALSE))
  expect_silent(corrplot(M, cl.pos = FALSE))
  expect_silent(corrplot(M, cl.pos = 'r'))
  expect_silent(corrplot(M, method = 'shade', addshade = 'all', cl.pos = 'b'))
})

test_that('Testing `tl.pos` parameter', {
  M = cor(mtcars)
  expect_silent(corrplot(M, tl.pos = TRUE))
  expect_silent(corrplot(M, tl.pos = FALSE))
  expect_silent(corrplot(M, tl.pos = 'd'))
  expect_silent(corrplot(M, tl.pos = 'n'))
  expect_silent(corrplot(M, tl.pos = 'lt'))
  expect_silent(corrplot(M, tl.pos = 'ld', type = 'lower'))
  expect_silent(corrplot(M, tl.pos = 'td', type = 'upper'))
})


test_that('Testing `col.lim` parameter', {
  M = cor(mtcars)
  expect_silent(corrplot(M, col.lim = c(-1, 1)))
  expect_error(corrplot(M, col.lim = c(0, 1)),
               regexp = 'color limits should cover matrix')
  expect_error(corrplot(M, col.lim = c(-1, 2)),
               regexp = 'col.lim should be within the interval')
})

test_that('Testing `tl.pos` parameter', {
  M = cor(mtcars)
  expect_silent(corrplot(M, tl.pos = 'td', type = 'upper'))
  expect_error(corrplot(M, tl.pos = 'td', type = 'lower'),
               regexp = 'type should be')
  expect_silent(corrplot(M, tl.pos = 'ld', type = 'lower'))
  expect_error(corrplot(M, tl.pos = 'ld', type = 'upper'),
               regexp = 'type should be')
})

test_that('Testing `corrRect` function', {
  M = cor(mtcars)
  corrplot(M, method = 'circle', order = 'FPC')
  expect_error(corrRect(c(5, 6)))
})

test_that('Testing `outline` parameter', {
  M = cor(mtcars)
  expect_silent(corrplot(M, outline = FALSE))
  expect_silent(corrplot(M, outline = TRUE))
  expect_silent(corrplot(M, outline = 'white'))

  for (unsupported in list(42, NA, NULL)) {
    expect_error(corrplot(M, outline = unsupported),
                 regexp = 'Unsupported value type for parameter outline')
  }

  expect_error(corrplot(M, outline = ''),
               regexp = 'invalid color name')

})

test_that('Issue #7: Enable to plot a matrix with NA', {
  M = cor(mtcars)
  diag(M) = NA
  expect_equal(corrplot(M)$corr, M)
})



test_that('Issue #20: plotmath expressions in rownames / colnames', {
  M = cor(mtcars)[1:5, 1:5]
  colnames(M) = c('alpha', 'beta', ':alpha+beta', ': a[0]', '=a[beta]')
  rownames(M) = c('alpha', 'beta', NA, '$a[0]', '$ a[beta]')
  corrplot(M)
})

test_that('Issue #20: using dollar sign in plotmath expressions', {
  M = cor(mtcars)
  rownames(M)[1] = ' $'
  corrplot(M)
})

test_that('Issue #21: plotCI=rect incompatible with some methods', {
  M = cor(mtcars)
  L = M - 0.1
  U = M + 0.1
  expect_equal(corrplot.mixed(M, lower = 'circle', upper = 'number',
                              lowCI = L, uppCI = U, plotCI = 'rect')$corr, M)
})

test_that('Issue #43: Return value should be the same as corrplot function', {
  M = cor(mtcars)
  expect_equal(corrplot.mixed(M)$corr, corrplot(M)$corr)
})

test_that('Should only work with matrix or dataframe', {
  expect_error(corrplot('some string'), regexp = 'matrix or data frame')
  expect_error(corrplot(42), regexp = 'matrix or data frame')
})

test_that('Non-correlation matrix', {
  M = matrix(runif(100, 0, 10), nrow = 10)
  expect_error(corrplot(M), regexp = 'The matrix is not in')
  expect_true(is.matrix(corrplot(M, is.corr = FALSE)$corr))
  expect_true(is.data.frame(corrplot(M, is.corr = FALSE)$corrPos))
})

test_that('Try different ordering', {
  M = cor(mtcars)

  expect_true(identical(M, corrplot(M)$corr))
  expect_false(identical(M, corrplot(M, order = 'AOE')))
  expect_false(identical(M, corrplot(M, order = 'FPC')))
  expect_false(identical(M, corrplot(M, order = 'hclust')))
  expect_false(identical(M, corrplot(M, order = 'alphabet')))

  expect_silent(corrplot(M, addrect = 2, order = 'hclust', type = 'full'))
})

test_that('Plot without a grid should not crash', {
  # TODO: currently, we cannot test how the rendered grid looks like
  # we can only check whether it does not crash
  M = cor(mtcars)

  # without grid
  expect_silent(corrplot(M, addgrid.col = NA))

  # white grid
  expect_silent(corrplot(M, addgrid.col = NULL, method = 'color'))
  expect_silent(corrplot(M, addgrid.col = NULL, method = 'shade'))

  # grey grid
  expect_silent(corrplot(M, addgrid.col = NULL, method = 'circle'))
})

test_that('Issue #46: Rendering NA values', {

  M = cor(mtcars)
  diag(M) = NA
  M[4, 2] = NA

  # default label for NAs
  expect_silent(corrplot(M))

  # black square instead of the label
  expect_silent(corrplot(M, na.label = 'square', na.label.col = 'black'))

  # large matrix
  M = matrix(runif(10000, 0.5, 1), nrow = 100)
  M[40:50, 30:70] = 0
  diag(M) = NA
  expect_silent(corrplot(M, method = 'color', cl.pos = 'n', tl.pos = 'n',
                         na.label = 'square', addgrid.col = NA))
})

test_that('Issue #55: Support for multiple characters when rendering NAs', {
  M = cor(mtcars)
  diag(M) = NA

  # label with 2 chars should work
  expect_silent(corrplot(M, na.label = 'NA'))

  expect_error(corrplot(M, na.label = 'ABC'),
               regexp = 'Maximum number of characters for NA label is: 2')

})

test_that('Using `number.digits` parameter', {
  M = cor(mtcars)

  expect_silent(corrplot(M, number.digits = 0))
  expect_silent(corrplot(M, number.digits = 1))
  # the allowed values for nsmall parameter of format() function is [0, 20]
  expect_silent(corrplot(M, method = 'number', number.digits = 20))

  expect_error(corrplot(M, number.digits = 1.2), regexp = 'is not TRUE')
  expect_error(corrplot(M, number.digits = -1), regexp = 'is not TRUE')
})

test_that('par() is restored after corrplot()', {
  grDevices::pdf(NULL)
  par1 = par('mar')
  corrplot(cor(mtcars))
  par2 = par('mar')
  dev.off()
  expect_identical(par1, par2)
})

test_that('Issue #79: Changing aspect ratio for the plot', {
  M = matrix(rnorm(70), ncol = 7)
  expect_silent(corrplot(M, is.corr = FALSE, win.asp = .7, method = 'circle'))
  expect_silent(corrplot(M, is.corr = FALSE, win.asp = .7, method = 'square'))
  expect_error(corrplot(M, is.corr = FALSE, win.asp = .7, method = 'pie'),
               regexp = 'supported only for circle and square methods')
})

test_that('Issue #18', {
  M = cor(mtcars)
  # TODO: calling the function without actually checking anything
  expect_silent(corrplot(M, method = 'pie', is.corr = FALSE, diag = FALSE))
  expect_silent(corrplot(M, method = 'pie', outline = TRUE))
  expect_silent(corrplot(M, method = 'pie', outline = 'white'))
})

test_that('Issue #76: separate `col` parameters corrplot.mixed', {
  M = cor(mtcars)
  expect_silent(corrplot.mixed(M, lower.col = 'black'))
  expect_silent(corrplot.mixed(M, lower = 'circle',
                               upper = 'number', upper.col = 'black'))
})

test_that('Issue #99: Mark significant correlations', {
  M = cor(mtcars)
  fakepmat = 1 - abs(M) ^ 0.2  # Hmisc::rcorr provides a p-value matrix, but
  # don't want to introduce the dependency
  expect_silent(corrplot(M, p.mat = fakepmat, insig = 'label_sig', pch = '!',
                         sig.level = c(0.001, 0.1, 0.99)))
  expect_silent(corrplot(M[1:2, ], p.mat = fakepmat[1:2, ], method = 'ellipse',
                         insig = 'label_sig', pch.col = 'white'))
  expect_silent(corrplot(M, p.mat = fakepmat, insig = 'label_sig',
                         pch = 'p<.05', pch.cex = 0.5, order = 'AOE'))
  expect_warning(corrplot(M, p.mat = fakepmat[, 11:1], insig = 'label_sig',
                         pch = 'p<.05', pch.cex = 0.5, order = 'AOE'))
})

test_that('col.lim', {
  M = cor(mtcars)
  expect_warning(corrplot(M*2, is.corr = FALSE, col.lim=c(-2, 2) * 2))
  expect_warning(corrplot(abs(M), is.corr = FALSE, col.lim=c(-1, 1)))
})


test_that("plotCI == 'circle'", {
  M = cor(mtcars)
  res = cor.mtest(mtcars, conf.level = 0.95)
  ## plot confidence interval(0.95), 'circle' method
  corrplot(M, p.mat = res$p, low = res$lowCI, upp = res$uppCI,
           plotCI = 'circle', addg = 'grey20', cl.pos = 'n')
  expect_error(corrplot(M, p.mat = res$p, plotCI = 'circle'),
               regexp = 'Need lowCI.mat and uppCI.mat!')
})

test_that("plotCI == 'square'", {
  M = cor(mtcars)
  res = cor.mtest(mtcars, conf.level = 0.95)
  ## plot confidence interval(0.95), 'circle' method
  corrplot(M, p.mat = res$p, low = res$lowCI, upp = res$uppCI, order = 'AOE',
           plotCI = 'square', addg = 'grey20', cl.pos = 'n')
})


test_that("add numbers", {
  M = cor(mtcars)
  corrplot(M, addCoef.col ='black')
})

test_that("p-value", {

  M = cor(mtcars)
  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 = 0.10, 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')
})


test_that("if (diag == 'n' && tl.pos != 'd')", {
  M = cor(mtcars)
  corrplot.mixed(M, diag = 'n', tl.pos = 'lt')
})


test_that('long name warning', {
  M = cor(mtcars)
  colnames(M) = rownames(M) = rep(toString(rep(LETTERS, 5)), 11)
  expect_warning(corrplot(M),  regexp = 'Not been able to calculate text margin')
})