DEGreport: Report of DEG analysis

# context("Plots")
# 
# data(humanGender)
# idx <- c(1:5, 75:80)
# counts <- assays(humanGender)[[1]]
# dse <- DESeqDataSetFromMatrix(counts[1:1000, idx],
#                               colData(humanGender)[idx,],
#                               design = ~group) %>% DESeq
# 
# res <- results(dse)
# 
# plot_cor <- function(dse){
#     ggplot(as.data.frame(counts(dse)),
#            aes(x = NA20502, y = NA20504)) +
#         geom_point() +
#         geom_cor(method = "kendall")
# }
# 
# # test_that("colors", {
# #     expect_equal(length(degColors(colData(dse))), 5)
# #     expect_equal(degColors(colData(dse), TRUE)[[2]] %>% class, "function")
# #     expect_equal(degColors(colData(dse), cat_values = c("red", "white"))[[1]],
# #                  c(Female = "red", Male = "white"))
# #     expect_error(degColors(data.frame(group = c("1", "2", "3")), palette = "Fake"))
# # })
# 
# test_that("degcovariates", {
#     resCov <- degCovariates(log2(counts(dse) + 0.5), colData(dse))
#     rows <- resCov[["corMatrix"]][resCov[["corMatrix"]][["fdr"]] < 0.05,"compare"]
#     rows <- rows[!is.na(rows)]
#     expect_true(length(rows) == 2)
#     expect_error(degCovariates(log2(counts(dse) + 0.5), colData(dse)[2:1,]))
# })
# 
# test_that("testGenes", {
#     expect_true(degPlotWide(dse, rownames(dse)[1:10], group = "group") %>%
#                     class %>% .[[2]] == "ggplot")
#     expect_true(degPlot(dse, res = res, n = 3, xs = "group", group = "group") %>%
#                     class %>% .[[2]] == "ggplot")
# })
# 
# test_that("singleFunctions", 
#     {
# 
#         expect_true(degMean(res[,4], counts(dse)) %>%
#                         class %>% .[[2]] == "ggplot")
#         expect_true(degVar(res[,4], counts(dse)) %>%
#                               class %>% .[[2]] == "ggplot")
#         expect_true(degMV(colData(dse)[["group"]], res[,4],
#                           counts(dse)) %>%
#                         class %>% .[[2]] == "ggplot")
#         detag <- row.names(res[1:10,])
#         expect_true(degMB(detag, colData(dse)[["group"]],
#                           counts(dse)) %>%
#                         class %>% .[[2]] == "ggplot")
#         expect_true(degVB(detag, colData(dse)[["group"]],
#                           counts(dse)) %>%
#                         class %>% .[[2]] == "ggplot")
#         expect_true(degVolcano(as.data.frame(res[,c("log2FoldChange", "pvalue")])) %>%
#                         class %>% .[[2]] == "ggplot")
#         expect_true(degPCA(counts(dse)) %>%
#                         class %>% .[[2]] == "ggplot")
#         expect_true(degMDS(counts(dse)) %>%
#                         class %>% .[[2]] == "ggplot")
#        
#         expect_true(plot_cor(dse) %>%
#                         class %>% .[[2]] == "ggplot")
#     })