From a4fd61388f85789acd0382d4a4770fd417fdf1ca Mon Sep 17 00:00:00 2001
From: Gavin Rhys Lloyd <grlloyd@users.noreply.github.com>
Date: Mon, 1 Jul 2024 12:07:17 +0100
Subject: [PATCH] fix broken tests

updated fold change to account for control_group param added to ttest
---
 DESCRIPTION                      |  2 +-
 R/fold_change_class.R            | 22 +++++++++++++++++++---
 tests/testthat/test-foldchange.R |  2 +-
 tests/testthat/test-ttest.R      |  6 +++---
 4 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 946c4ca..3a939cc 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: structToolbox
 Type: Package
 Title: Data processing & analysis tools for Metabolomics and other omics
-Version: 1.17.2
+Version: 1.17.3
 Authors@R: c(
     person(
         c("Gavin","Rhys"),
diff --git a/R/fold_change_class.R b/R/fold_change_class.R
index ec345d9..77fb790 100644
--- a/R/fold_change_class.R
+++ b/R/fold_change_class.R
@@ -199,7 +199,7 @@ setMethod(f="model_apply",
         
         counter=1
         
-        D$sample_meta[[M$factor_name]]=ordered(D$sample_meta[[M$factor_name]])
+        D$sample_meta[[M$factor_name]]=factor(D$sample_meta[[M$factor_name]])
         
         # for all pairs of groups
         for (A in 1:(length(L)-1)) {
@@ -209,12 +209,28 @@ setMethod(f="model_apply",
                 FG=filter_smeta(factor_name=M$factor_name,mode='include',levels=L[c(A,B)])
                 FG=model_apply(FG,D)
                 # change to ordered factor so that we make use of control group
-                FG$filtered$sample_meta[[M$factor_name]]=ordered(FG$filtered$sample_meta[[M$factor_name]],levels=L[c(A,B)])
+                #FG$filtered$sample_meta[[M$factor_name]]=ordered(FG$filtered$sample_meta[[M$factor_name]],levels=L[c(A,B)])
                 
                 if (M$method=='geometric') {
                     
+                    control_group = NULL
+                    if (length(M$control_group)>0) {
+                        if (L[B] == M$control_group) {
+                            control_group = M$control_group
+                            
+                        }
+                    }
+
                     # apply t-test
-                    TT=ttest(alpha=0.05,mtc='none',factor_names=M$factor_name,paired=M$paired,paired_factor=M$sample_name,conf_level=M$conf_level)
+                    TT=ttest(
+                        alpha=0.05,
+                        mtc='none',
+                        factor_names=M$factor_name,
+                        paired=M$paired,
+                        paired_factor=M$sample_name,
+                        conf_level=M$conf_level,
+                        control_group=control_group)
+                    
                     TT=model_apply(TT,predicted(FG))
                     # log2(fold change) is the difference in estimate.mean from ttest
                     if (M$paired) {
diff --git a/tests/testthat/test-foldchange.R b/tests/testthat/test-foldchange.R
index 05e14fb..667addb 100644
--- a/tests/testthat/test-foldchange.R
+++ b/tests/testthat/test-foldchange.R
@@ -17,7 +17,7 @@ test_that('fold_change',{
   D$data[1:25,3] = NA
   
   # unpaired
-  FF = fold_change(factor_name='Species',method="geometric")
+  FF = fold_change(factor_name='Species',method="geometric",control_group='versicolor')
   FF = model_apply(FF,D)
   m=exp(mean(log(D$data[D$sample_meta$Species=='virginica',1]))) / exp(mean(log((D$data[D$sample_meta$Species=='versicolor',1]))))
   expect_equal(FF$fold_change[1,1],m,tolerance=0.00001)
diff --git a/tests/testthat/test-ttest.R b/tests/testthat/test-ttest.R
index ff3ca61..6cacf8a 100644
--- a/tests/testthat/test-ttest.R
+++ b/tests/testthat/test-ttest.R
@@ -8,7 +8,7 @@ test_that('ttest',{
     ttest(factor_names='Species')
   # apply
   M = model_apply(M,D)
-  expect_equal(M[2]$t_statistic[1,1],-15.386,tolerance=0.0005)
+  expect_equal(M[2]$t_statistic[1,1],15.386,tolerance=0.0005)
 })
 
 
@@ -68,11 +68,11 @@ test_that('paired-ttest',{
   
   # 50 pairs - 1 without pair - 1 with an NA - 1 for ttest
   expect_equal(M$dof[1],47) 
-  expect_equal(M$t_statistic[1,1],-5.195,tolerance=0.0005)
+  expect_equal(M$t_statistic[1,1],5.195,tolerance=0.0005)
   
   # 50 pairs - 1 without pair - 1 for ttest
   expect_equal(M$dof[2],48) 
-  expect_equal(M$t_statistic[2,1],-3.014,tolerance=0.0005)
+  expect_equal(M$t_statistic[2,1],3.014,tolerance=0.0005)
   
   # check order dependence
   expect_equal(M$t_statistic[1,1],M2$t_statistic[1,1],tolerance=0.00005)