From e3434b3b69e0b2055bd6064173026581226e3d03 Mon Sep 17 00:00:00 2001
From: mikejiang <wjiang2@fhcrc.org>
Date: Fri, 7 Oct 2016 14:37:04 -0700
Subject: [PATCH] add unit test for 1d flowClust

---
 tests/testthat.R         |   9 +++
 tests/testthat/test_1d.R | 121 +++++++++++++++++++++++++++++++++++++++
 2 files changed, 130 insertions(+)
 create mode 100644 tests/testthat.R
 create mode 100644 tests/testthat/test_1d.R

diff --git a/tests/testthat.R b/tests/testthat.R
new file mode 100644
index 0000000..51f3278
--- /dev/null
+++ b/tests/testthat.R
@@ -0,0 +1,9 @@
+library(testthat)
+library(flowClust)
+library(parallel)
+test_check("flowClust")
+
+#devtools::test("~/rglab/workspace/flowClust")
+
+#taking quite some time , thus only for internal testing
+#test_file("~/rglab/workspace/flowClust/tests/testthat/flowClust-gated-data.R")
diff --git a/tests/testthat/test_1d.R b/tests/testthat/test_1d.R
new file mode 100644
index 0000000..6c3db0e
--- /dev/null
+++ b/tests/testthat/test_1d.R
@@ -0,0 +1,121 @@
+context("1d clustering")
+data(GvHD)
+fr <- transform(GvHD[[1]], transformList(c("FL1-H"),  log))
+trans <- estimateLogicle(fr, c("FL1-H", "FL2-H", "FL3-H", "FL4-H", "FL2-A"))
+fr <- transform(fr, trans)
+
+options("mc.cores" = 4)
+test_that("flowClust:SSH-H, 1 mode", {
+  chnl <- "SSC-H"
+  res <- flowClust(fr, varNames = chnl, tol = 1e-7, K = 2)
+  expect_equal(res@mu, matrix(c(5.27, 6.84), nrow = 2), tol = 5e-2)
+  expect_equal(res@w, c(0.286, 0.713), tol = 3e-2)
+  
+  #relax tol to see the worse fit
+  res <- flowClust(fr, varNames = chnl, tol = 1e-5, K = 2)
+  expect_equal(res@mu, matrix(c(5.27, 6.84), nrow = 2), tol = 0.3)
+  expect_equal(res@w, c(0.286, 0.713), tol = 0.16)
+  
+  #fiddle with randomStart to change the fit
+  res <- flowClust(fr, varNames = chnl, tol = 1e-10, K = 2, randomStart = 10)
+  expect_equal(res@mu, matrix(c(5.27, 6.84), nrow = 2), tol = 5e-3)
+  expect_equal(res@w, c(0.286, 0.713), tol = 2e-3)
+  
+  #tmixture
+  g <- tmixFilter(parameters = chnl, tol = 1e-10, K = 2, randomStart = 10)
+  res.g <- filter(fr, g)
+  res.g <- as(res.g, "flowClust")
+  res.g@varNames <- as.vector(res.g@varNames)
+  expect_equal(res, res.g)
+  
+  #run through K=1:4
+  res <- flowClust(fr, varNames = chnl, tol = 1e-10, K = 1:4, randomStart = 0)
+  expect_equal(res[[2]]@mu, matrix(c(5.27, 6.84), nrow = 2), tol = 5e-3)
+  expect_equal(res[[2]]@w, c(0.286, 0.713), tol = 6e-4)
+  
+  
+  expect_equal(res[[1]]@mu, matrix(c(6.4), nrow = 1), tol = 6e-3)
+  
+  #k = 1 is expected to be the best fit
+  scores <- sapply(res, slot, "ICL")
+  #ICLs decrease as K increases
+  expect_true(all(diff(scores) <0))
+  
+  # par(mfrow=c(1,4))
+  # for(obj in res)
+  #  hist(obj, fr, main = paste("ICL:", round(obj@ICL),"BIC:", round(obj@BIC)))
+  
+  
+})
+
+
+test_that("flowClust:FL1-H, 2 mode", {
+  
+  chnl <- "FL1-H"
+  
+  res <- flowClust(fr, varNames = chnl, tol = 1e-10, K = 1:4, randomStart = 0)
+  
+  #K=1
+  expect_equal(res[[1]]@mu, matrix(c(21.6), nrow = 1), tol = 0.001)
+  
+  #K=2
+  expect_equal(res[[2]]@mu, matrix(c(49.15, 82.82), nrow = 2), tol = 0.001)
+  expect_equal(res[[2]]@w, c(0.689, 0.31), tol = 7e-4)
+  
+  #K=3
+  expect_equal(res[[3]]@mu, matrix(c(23.1, 30.8, 44.5), nrow = 3), tol = 0.001)
+  expect_equal(res[[3]]@w, c(0.2707028, 0.4088046, 0.3204925), tol = 7e-4)
+  
+  
+  #2 mode is best fit
+  scores <- sapply(res, slot, "ICL")
+  scores.diff <- diff(scores)
+  expect_gt(scores.diff[1], 0) #1st is pos
+  expect_true(all(scores.diff[-1] <0))# the rest are neg
+  
+  # par(mfrow=c(1,4))
+  # for(obj in res)
+  #  hist(obj, fr, main = paste("ICL:", round(obj@ICL),"BIC:", round(obj@BIC)))
+  
+})
+
+test_that("flowClust:FL2-H, 3 mode", {
+  chnl <- "FL2-H"
+  
+  res <- flowClust(fr, varNames = chnl, tol = 1e-10, K = 1:4, randomStart = 0)
+  expect_equal(res[[1]]@mu, matrix(c(1.820132), nrow = 1), tol = 0.001)
+  
+  expect_equal(res[[2]]@mu, matrix(c(1.610172, 3.148424), nrow = 2), tol = 0.001)
+  expect_equal(res[[2]]@w, c(0.769645, 0.230355), tol = 7e-4)
+  
+  expect_equal(res[[3]]@mu, matrix(c(-0.09441319, 1.21476765, 1.91313389), nrow = 3), tol = 0.001)
+  expect_equal(res[[3]]@w, c(0.1041290, 0.6273802, 0.2684908), tol = 7e-4)
+  
+  
+  
+  #3 mode is best fit
+  scores <- sapply(res, slot, "ICL")
+  scores.diff <- diff(scores)
+  expect_gt(scores.diff[2], 0) #2nd is pos
+  expect_true(all(scores.diff[-2] < 0))# the rest are neg
+  # par(mfrow=c(1,4))
+  # for(obj in res)
+  #  hist(obj, fr, main = paste("ICL:", round(obj@ICL),"BIC:", round(obj@BIC)))
+})
+
+test_that("flowClust:FL2-A, 3 mode", {
+  chnl <- "FL2-A"
+  
+  res <- flowClust(fr, varNames = chnl, tol = 1e-10, K = 1:4, randomStart = 0)
+  
+  #3 mode is best fit
+  scores <- sapply(res, slot, "ICL")
+  scores.diff <- diff(scores)
+  # expect_gt(scores.diff[2], 0) #2nd is pos
+  # expect_true(all(scores.diff[-2] < 0))# the rest are neg
+  # par(mfrow=c(1,4))
+  # for(obj in res)
+  #  hist(obj, fr, main = paste("ICL:", round(obj@ICL),"BIC:", round(obj@BIC)))
+})
+
+