Nothing
library('ggplot2')
library('vdiffr')
geneNames = paste0('gene_', 1:2)
genCors = function() {
ematNow = rbind(c(1, 0.9, 0.8, 1, 0.9, 0.8), c(1, 0.9, 0.8, -1, -0.9, -0.8))
rownames(ematNow) = geneNames
groupVec = c('a' ,'a', 'a', 'b', 'b', 'b')
cors = calcCorr(ematNow, groupVec)
return(cors)}
test_that('calcDist', {
d = calcDist(c(1, 0), c(1, 0))
expect_equal(d, 0)
d = calcDist(c(1, 0), c(0, 1))
expect_equal(d, sqrt(2))
})
test_that('calcCCDSimple', {
ccd = calcCCDSimple(diag(1, 2), diag(1, 2))
expect_equal(ccd, 1)
ref = cbind(c(1, 1), c(1, 1))
emat = rbind(c(1, 0, 1), c(0, 1, 0))
ccd = calcCCDSimple(ref, emat)
expect_equal(ccd, 2)
ref = cbind(c(1, 0, -1), c(0, 1, -1), c(-1, -1, 1))
emat = rbind(c(1, 0, 0), c(0, 1, -1), c(0, 1, 1))
ccd = calcCCDSimple(ref, emat, scale = TRUE)
expect_equal(ccd, 1/3)
})
test_that('checkVar', {
groupVec = c('a', 'a', 'b', 'b')
emat = cbind(diag(1, 2), diag(1, 2))
expect_invisible(checkVar(emat, groupVec))
emat = cbind(diag(1, 2), matrix(1, 2, 2))
rownames(emat) = paste0('gene_', 1:2)
expect_error(
checkVar(emat, c('a', 'a', 'b', 'b')),
paste0('Zero variance in 2 gene-group pairs. ',
'See _deltaccd_zero_var_genes.csv for full list.'), fixed = TRUE)
})
test_that('checkGenes', {
emat = diag(1, 2)
rownames(emat) = geneNames
refCor = emat
rownames(refCor) = geneNames
expect_equal(checkGenes(emat, refCor), geneNames)
refCor = diag(1, 4)
rownames(refCor) = paste0('gene_', 1:4)
expect_error(
checkGenes(emat, refCor),
paste0('2 gene(s) is/are not in the expression matrix. ',
'See _deltaccd_missing_genes.csv for full list.'), fixed = TRUE)
emat = diag(1, 6)
refCor = diag(1, 4)
geneNames2 = paste0('gene_', 1:6)
rownames(emat) = geneNames2
rownames(refCor) = geneNames2[1:4]
expect_equal(checkGenes(emat, refCor, geneNames2[1:5]), geneNames2[1:4])
})
test_that('checkRefCor', {
refCor = diag(1, 2)
rownames(refCor) = geneNames
colnames(refCor) = rownames(refCor)
expect_equal(checkRefCor(refCor), refCor)
expect_error(checkRefCor(), 'Either refCor or refEmat must be supplied.',fixed = TRUE)
rownames(refCor) = paste0('gene_', 3:4)
expect_error(checkRefCor(refCor),
'refCor must be a correlation matrix, with identical rownames and colnames.',
fixed = TRUE)
refCor = rbind(c(1, 0, 0), c(1, 0, 0))
expect_error(checkRefCor(refCor),
'refCor must be a correlation matrix, with identical rownames and colnames.',
fixed = TRUE)
})
test_that('calcDeltaCCDSimple', {
ref = cbind(c(1, -1), c(-1, 1))
emat = ref
expect_equal(calcDeltaCCDSimple(ref, emat, 1:2), 0)
})
test_that('makePerms', {
perms = makePerms(1:10)
expect_equal(dim(perms), c(1000, 10))
})
test_that('calcCorr', {
cors = genCors()
expect_equal(cors, data.table(group = c('a', 'b', 'a', 'b'),
gene1 = factor(paste0('gene_', c(2, 2, 1, 1))),
gene2 = factor(paste0('gene_', c(1, 1, 2, 2)),
levels = paste0('gene_', 2:1)),
rho = c(1, -1, 1, -1)))
})
test_that('calcColorLimits', {
cors = genCors()
cLims = calcColorLimits(cors$rho)
expect_equal(cLims, c('#E66101', '#5E3C99'))
})
test_that('plotHeatmapSimple', {
cors = genCors()
cLims = calcColorLimits(cors$rho)
p = plotHeatmapSimple(
ggplot(cors) + facet_wrap(vars(group)), cLims)
expect_doppelganger('basic heatmap', p)
})
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