Committed tests for cosinor based analysis.

tests/testthat/test-compareRhythms_cosinor.R

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+context("compareRhythms_cosinor")
+
+load("test_data_ma.rda")
+
+test_that("cosinor analysis works for default params and independent sampling", {
+  results <- compareRhythms(expr, exp_design, method = "cosinor")
+  expect_s3_class(results, "data.frame")
+  expect_named(results,
+               c("id", "category", "rhythmic_in_CC", "rhythmic_in_KD", "diff_rhythmic"))
+})
+
+test_that("cosinor analysis works for different input params", {
+  expect_error(compareRhythms(expr, exp_design, period = 12, method = "cosinor"))
+  expect_s3_class(compareRhythms(expr, exp_design, rhythm_fdr = 0.01, method = "cosinor"), "data.frame")
+  expect_s3_class(compareRhythms(expr, exp_design, compare_fdr = 0.01, method = "cosinor"), "data.frame")
+  expect_s3_class(compareRhythms(expr, exp_design, rhythm_fdr = 0.1, compare_fdr = 0.01, method = "cosinor"), "data.frame")
+  expect_s3_class(compareRhythms(expr, exp_design, amp_cutoff = 0, method = "cosinor"), "data.frame")
+  expect_error(compareRhythms(expr, exp_design, rhythm_fdr = 0, method = "cosinor"))
+  results <- compareRhythms(expr, exp_design, just_classify = FALSE, method = "cosinor")
+  expect_s3_class(results, "data.frame")
+  expect_named(results,
+               c("id", "category", "rhythmic_in_CC", "rhythmic_in_KD", "diff_rhythmic", "CC_amp",
+                 "CC_phase", "KD_amp", "KD_phase", "adj_p_val_CC_or_KD", "adj_p_val_DR"))
+})
+
+test_that("cosinor analysis runs for arrhythmic dataset", {
+  dim_y <- dim(expr)
+  y_null <- matrix(0, nrow = dim_y[1], ncol = dim_y[2])
+  colnames(y_null) <- colnames(expr)
+  rownames(y_null) <- rownames(expr)
+  expect_error(compareRhythms(y_null, exp_design, method = "cosinor"))
+})
+
+exp_design <- dplyr::mutate(dplyr::group_by(exp_design, group, time), ID = dplyr::row_number())
+exp_design$ID <- factor(exp_design$ID)
+
+test_that("longitudinal cosinor analysis works for default params and independent sampling", {
+  results <- compareRhythms(expr, exp_design, method = "cosinor", longitudinal = TRUE)
+  expect_s3_class(results, "data.frame")
+  expect_named(results,
+               c("id", "category", "rhythmic_in_CC", "rhythmic_in_KD", "diff_rhythmic"))
+})
+
+test_that("cosinor analysis works for different input params", {
+  expect_error(compareRhythms(expr, exp_design, period = 12, method = "cosinor", longitudinal = TRUE))
+  expect_s3_class(compareRhythms(expr, exp_design, rhythm_fdr = 0.01, method = "cosinor", longitudinal = TRUE), "data.frame")
+  expect_s3_class(compareRhythms(expr, exp_design, compare_fdr = 0.01, method = "cosinor", longitudinal = TRUE), "data.frame")
+  expect_s3_class(compareRhythms(expr, exp_design, rhythm_fdr = 0.1, compare_fdr = 0.01, method = "cosinor", longitudinal = TRUE), "data.frame")
+  expect_s3_class(compareRhythms(expr, exp_design, amp_cutoff = 0, method = "cosinor", longitudinal = TRUE), "data.frame")
+  expect_error(compareRhythms(expr, exp_design, rhythm_fdr = 0, method = "cosinor", longitudinal = TRUE))
+  results <- compareRhythms(expr, exp_design, just_classify = FALSE, method = "cosinor", longitudinal = TRUE)
+  expect_s3_class(results, "data.frame")
+  expect_named(results,
+               c("id", "category", "rhythmic_in_CC", "rhythmic_in_KD", "diff_rhythmic", "CC_amp",
+                 "CC_phase", "KD_amp", "KD_phase", "adj_p_val_CC_or_KD", "adj_p_val_DR"))
+})
+
+test_that("cosinor analysis runs for arrhythmic dataset", {
+  dim_y <- dim(expr)
+  y_null <- matrix(0, nrow = dim_y[1], ncol = dim_y[2])
+  colnames(y_null) <- colnames(expr)
+  rownames(y_null) <- rownames(expr)
+  expect_error(compareRhythms(y_null, exp_design, method = "cosinor", longitudinal = TRUE))
+})
+
+