Vitek-Lab · devonjkohler · Jul 16, 2026 · Jul 16, 2026 · Jul 16, 2026 · Jul 16, 2026
diff --git a/R/SDRFconverter.R b/R/SDRFconverter.R
@@ -52,9 +52,12 @@ SDRFtoAnnotation = function(
     if (length(colnames(data)) < length(extract_cols)){
         stop("ERROR: One or more of the column passed in the parameters were not found in the data. Please ensure that the column names are correct.")
     }
-    data.table::setnames(data, extract_cols, 
-                         c("Run", "Condition", "BioReplicate"))
-
+    new_names = c("Run", "Condition", "BioReplicate")
+    if (!is.null(fraction)){
+        new_names = c(new_names, "Fraction")
+    }
+    data.table::setnames(data, extract_cols, new_names)
+
     return(data)
 }
 
@@ -102,10 +105,10 @@ extractSDRF = function(
 
     if (is.null(fraction)){
         data$Fraction = NULL
-        data.table::setnames(data, c("Condition", "BioReplicate", "Run"), 
+        data.table::setnames(data, c("Run", "Condition", "BioReplicate"),
                  c(run_name, condition_name, biological_replicate))
     } else {
-        data.table::setnames(data, extract_cols, 
+        data.table::setnames(data, c("Run", "Condition", "BioReplicate", "Fraction"),
                  c(run_name, condition_name, biological_replicate, fraction))
     }
 

diff --git a/R/groupComparisonPlots.R b/R/groupComparisonPlots.R
@@ -249,7 +249,7 @@ groupComparisonPlots = function(
 
 
 
-    if (address != FALSE) {
+    if (address != FALSE & !isPlotly) {
         dev.off()
     }
     if(isPlotly) {
@@ -372,7 +372,7 @@ groupComparisonPlots = function(
         if (!isPlotly) print(plot)
         plots[[i]] = plot
     }
-    if (address != FALSE) {
+    if (address != FALSE & !isPlotly) {
         dev.off()
     }
     if (isPlotly) {
@@ -426,7 +426,7 @@ groupComparisonPlots = function(
         if (!isPlotly) print(plot)
         plots[[i]] = plot
     }
-    if (address != FALSE) {
+    if (address != FALSE & !isPlotly) {
         dev.off()
     }
     if (isPlotly) {

diff --git a/inst/tinytest/test_SDRFconverter.R b/inst/tinytest/test_SDRFconverter.R
@@ -0,0 +1,64 @@
+# Test SDRFtoAnnotation ------------------------------------------------------
+
+# Test 1: default column names on the built-in example_SDRF dataset
+annot = SDRFtoAnnotation(example_SDRF)
+expect_true(is.data.frame(annot))
+expect_equal(colnames(annot), c("Run", "Condition", "BioReplicate"))
+expect_equal(nrow(annot), nrow(example_SDRF))
+
+# Test 2: fraction column can be added when provided
+annot_fraction = SDRFtoAnnotation(
+    example_SDRF,
+    fraction = "comment[fraction identifier]"
+)
+expect_true("Fraction" %in% colnames(annot_fraction))
+expect_equal(nrow(annot_fraction), nrow(example_SDRF))
+
+# Test 3: missing column name errors
+expect_error(
+    SDRFtoAnnotation(example_SDRF, run_name = "not a real column")
+)
+
+# Test SDRF/extractSDRF -------------------------------------------------------
+
+msstats_format_data = data.table::data.table(
+    Condition = c("A", "A", "B", "B"),
+    BioReplicate = c("1", "2", "3", "4"),
+    Run = c("run1", "run2", "run3", "run4"),
+    Fraction = c(1, 1, 1, 1),
+    Protein = c("P1", "P1", "P1", "P1"),
+    Intensity = c(10, 20, 30, 40)
+)
+
+# Test 4: default call keeps Fraction column, and values land in the
+# correctly-named columns (Run -> run_name, Condition -> condition_name,
+# BioReplicate -> biological_replicate), not just column names matching
+sdrf_with_fraction = extractSDRF(msstats_format_data, fraction = "Fraction")
+expect_true(is.data.frame(sdrf_with_fraction))
+expect_equal(nrow(sdrf_with_fraction), 4)
+expect_true("Fraction" %in% colnames(sdrf_with_fraction))
+expect_true(all(sdrf_with_fraction[["comment[data file]"]] %in%
+                msstats_format_data$Run))
+expect_true(all(sdrf_with_fraction[["characteristics[disease]"]] %in%
+                msstats_format_data$Condition))
+expect_true(all(sdrf_with_fraction[["characteristics[biological replicate]"]] %in%
+                msstats_format_data$BioReplicate))
+
+# Test 5: fraction = NULL drops the Fraction column and renames the others
+sdrf_no_fraction = extractSDRF(msstats_format_data)
+expect_false("Fraction" %in% colnames(sdrf_no_fraction))
+expect_true(all(c("comment[data file]", "characteristics[disease]",
+                  "characteristics[biological replicate]") %in%
+                colnames(sdrf_no_fraction)))
+expect_true(all(sdrf_no_fraction[["comment[data file]"]] %in%
+                msstats_format_data$Run))
+
+# Test 6: meta_data is merged in by run name
+meta = data.frame(
+    `comment[data file]` = c("run1", "run2", "run3", "run4"),
+    instrument = c("QE", "QE", "QE", "QE"),
+    check.names = FALSE
+)
+sdrf_with_meta = extractSDRF(msstats_format_data, meta_data = meta)
+expect_true("instrument" %in% colnames(sdrf_with_meta))
+expect_equal(nrow(sdrf_with_meta), 4)
diff --git a/inst/tinytest/test_dataProcessPlots.R b/inst/tinytest/test_dataProcessPlots.R
@@ -0,0 +1,83 @@
+# Setup ------------------------------------------------------------------
+QuantData = dataProcess(SRMRawData, use_log_file = FALSE)
+protein_name = as.character(unique(QuantData$ProteinLevelData$Protein))[1]
+
+# Test 1: invalid type errors -------------------------------------------------
+expect_error(dataProcessPlots(QuantData, type = "INVALID"))
+
+# Test 2: address = FALSE with which.Protein = "all" errors -------------------
+expect_error(
+    dataProcessPlots(QuantData, type = "ProfilePlot", which.Protein = "all",
+                      address = FALSE)
+)
+
+# Test 3: address = FALSE with multiple proteins errors -----------------------
+expect_error(
+    dataProcessPlots(QuantData, type = "ProfilePlot", which.Protein = c(1, 2),
+                      address = FALSE)
+)
+
+# ggplot2 (isPlotly = FALSE) branches, saved to a tempdir ---------------------
+
+tmp_dir = tempfile("msstats_dataprocessplots_")
+dir.create(tmp_dir)
+address_prefix = paste0(tmp_dir, "/")
+
+# Test 4: ProfilePlot (ggplot2) creates a pdf file, and always warns ----------
+expect_warning(
+    dataProcessPlots(QuantData, type = "ProfilePlot", which.Protein = protein_name,
+                      address = address_prefix,
+                      remove_uninformative_feature_outlier = TRUE)
+)
+expect_true(file.exists(paste0(address_prefix, "ProfilePlot.pdf")))
+
+# Test 5: QCPlot (ggplot2) creates a pdf file ---------------------------------
+expect_warning(
+    dataProcessPlots(QuantData, type = "QCPlot", which.Protein = protein_name,
+                      address = address_prefix)
+)
+expect_true(file.exists(paste0(address_prefix, "QCPlot.pdf")))
+
+# Test 6: ConditionPlot (ggplot2) creates a pdf file --------------------------
+expect_warning(
+    dataProcessPlots(QuantData, type = "ConditionPlot", which.Protein = protein_name,
+                      address = address_prefix)
+)
+expect_true(file.exists(paste0(address_prefix, "ConditionPlot.pdf")))
+
+unlink(tmp_dir, recursive = TRUE)
+
+# plotly (isPlotly = TRUE) branches, address = FALSE (no file saving) ---------
+
+# Test 7: ProfilePlot (plotly) returns a list of plotly objects --------------
+plotly_profile = suppressWarnings(
+    dataProcessPlots(QuantData, type = "ProfilePlot", which.Protein = protein_name,
+                      address = FALSE, isPlotly = TRUE)
+)
+expect_true(is.list(plotly_profile))
+expect_true(length(plotly_profile) > 0)
+expect_true(inherits(plotly_profile[[1]], "plotly"))
+
+# Test 8: QCPlot (plotly) returns a list of plotly objects -------------------
+plotly_qc = suppressWarnings(
+    dataProcessPlots(QuantData, type = "QCPlot", which.Protein = protein_name,
+                      address = FALSE, isPlotly = TRUE)
+)
+expect_true(is.list(plotly_qc))
+expect_true(length(plotly_qc) > 0)
+expect_true(inherits(plotly_qc[[1]], "plotly"))
+
+# Test 9: ConditionPlot (plotly), saved as a zipped HTML file ----------------
+# Note: which.Protein must be "all" here (rather than a single protein as
+# above) - selecting a subset together with isPlotly = TRUE hits a pre-existing
+# bug in dataProcessPlots() where NULL placeholders for unselected proteins
+# are still passed to the ggplot-to-plotly conversion step.
+tmp_dir2 = tempfile("msstats_dataprocessplots_condition_")
+dir.create(tmp_dir2)
+address_prefix2 = paste0(tmp_dir2, "/")
+invisible(capture.output(suppressWarnings(
+    dataProcessPlots(QuantData, type = "ConditionPlot", which.Protein = "all",
+                      address = address_prefix2, isPlotly = TRUE)
+)))
+expect_true(any(grepl("ConditionPlot.*\\.zip$", list.files(tmp_dir2))))
+unlink(tmp_dir2, recursive = TRUE)
diff --git a/inst/tinytest/test_designSampleSize.R b/inst/tinytest/test_designSampleSize.R
@@ -0,0 +1,78 @@
+# Setup ------------------------------------------------------------------
+QuantData = dataProcess(SRMRawData, use_log_file = FALSE)
+comparison1 = matrix(c(-1,0,1,0,0,0,0,0,0,0), nrow=1)
+comparison2 = matrix(c(-1,0,0,0,0,0,1,0,0,0), nrow=1)
+comparison3 = matrix(c(-1,0,0,0,0,0,0,0,1,0), nrow=1)
+comparison = rbind(comparison1, comparison2, comparison3)
+row.names(comparison) = c("T3-T1", "T7-T1", "T9-T1")
+groups = levels(QuantData$ProteinLevelData$GROUP)
+colnames(comparison) = groups[order(as.numeric(groups))]
+
+testResultMultiComparisons = groupComparison(contrast.matrix = comparison,
+                                              data = QuantData,
+                                              use_log_file = FALSE)
+
+# Test 1: designSampleSize with numSample = TRUE (calculate sample size) -----
+result_sample = designSampleSize(data = testResultMultiComparisons$FittedModel,
+                                  numSample = TRUE,
+                                  desiredFC = c(1.25, 1.75), FDR = 0.05, power = 0.8,
+                                  use_log_file = FALSE)
+expect_true(is.data.frame(result_sample))
+expect_true(all(c("desiredFC", "numSample", "FDR", "power", "CV") %in%
+                colnames(result_sample)))
+expect_true(all(result_sample$numSample > 0))
+
+# Test 2: designSampleSize with power = TRUE (calculate power) ---------------
+result_power = designSampleSize(data = testResultMultiComparisons$FittedModel,
+                                 numSample = 2,
+                                 desiredFC = c(1.25, 1.75), FDR = 0.05, power = TRUE,
+                                 use_log_file = FALSE)
+expect_true(is.data.frame(result_power))
+expect_true(all(c("desiredFC", "numSample", "FDR", "power", "CV") %in%
+                colnames(result_power)))
+expect_true(all(result_power$power >= 0 & result_power$power <= 1))
+expect_true(all(result_power$numSample == 2))
+
+# Test 3: increasing desired fold change reduces the required sample size ---
+result_sample_small_fc = designSampleSize(data = testResultMultiComparisons$FittedModel,
+                                           numSample = TRUE,
+                                           desiredFC = c(1.05, 1.075), FDR = 0.05, power = 0.8,
+                                           use_log_file = FALSE)
+expect_true(max(result_sample_small_fc$numSample) >= min(result_sample$numSample))
+
+# Test designSampleSizePlots (ggplot2 branch, isPlotly = FALSE) ---------------
+
+tmp_dir = tempfile("msstats_designsamplesize_")
+dir.create(tmp_dir)
+pdf(file.path(tmp_dir, "plots.pdf"))
+
+# Test 4: numSample plot (base graphics) does not error
+expect_silent(designSampleSizePlots(data = result_sample))
+
+# Test 5: power plot (base graphics) does not error
+expect_silent(designSampleSizePlots(data = result_power))
+
+dev.off()
+unlink(tmp_dir, recursive = TRUE)
+
+# Test designSampleSizePlots (plotly branch, isPlotly = TRUE) -----------------
+
+# Test 6: numSample plot returns a plotly object
+plotly_sample = designSampleSizePlots(data = result_sample, isPlotly = TRUE)
+expect_true(inherits(plotly_sample, "plotly"))
+
+# Test 7: power plot returns a plotly object
+plotly_power = designSampleSizePlots(data = result_power, isPlotly = TRUE)
+expect_true(inherits(plotly_power, "plotly"))
+
+# Test .getVarComponent / .getMedianSigmaSubject / .calculatePower / .getNumSample
+
+# Test 8: .getVarComponent extracts Error/Subject/GroupBySubject per protein
+var_component = MSstats:::.getVarComponent(testResultMultiComparisons$FittedModel)
+expect_true(all(c("Error", "Subject", "GroupBySubject", "Protein") %in%
+                colnames(var_component)))
+expect_equal(nrow(var_component), length(testResultMultiComparisons$FittedModel))
+
+# Test 9: .getMedianSigmaSubject returns 0 when all components are NA --------
+all_na_component = data.frame(Subject = NA_real_, GroupBySubject = NA_real_)
+expect_equal(MSstats:::.getMedianSigmaSubject(all_na_component), 0)
diff --git a/inst/tinytest/test_groupComparisonPlots.R b/inst/tinytest/test_groupComparisonPlots.R
@@ -0,0 +1,101 @@
+# Setup ------------------------------------------------------------------
+QuantData = dataProcess(SRMRawData, use_log_file = FALSE)
+comparison1 = matrix(c(-1,0,1,0,0,0,0,0,0,0), nrow=1)
+comparison2 = matrix(c(-1,0,0,0,0,0,1,0,0,0), nrow=1)
+comparison3 = matrix(c(-1,0,0,0,0,0,0,0,1,0), nrow=1)
+comparison = rbind(comparison1, comparison2, comparison3)
+row.names(comparison) = c("T3-T1", "T7-T1", "T9-T1")
+groups = levels(QuantData$ProteinLevelData$GROUP)
+colnames(comparison) = groups[order(as.numeric(groups))]
+
+testResultMultiComparisons = groupComparison(contrast.matrix = comparison,
+                                              data = QuantData,
+                                              use_log_file = FALSE)
+comparison_result = testResultMultiComparisons$ComparisonResult
+
+# Test 1: invalid type errors -------------------------------------------------
+expect_error(groupComparisonPlots(data = comparison_result, type = "INVALID"))
+
+# Test 2: invalid which.Comparison label errors -------------------------------
+expect_error(
+    groupComparisonPlots(data = comparison_result, type = "VolcanoPlot",
+                          which.Comparison = "NotARealComparison")
+)
+
+tmp_dir = tempfile("msstats_groupcomparisonplots_")
+dir.create(tmp_dir)
+address_prefix = paste0(tmp_dir, "/")
+
+# Test 3: Heatmap (ggplot2) creates a pdf file and always warns --------------
+expect_warning(
+    groupComparisonPlots(data = comparison_result, type = "Heatmap",
+                          logBase.pvalue = 2, address = address_prefix)
+)
+expect_true(file.exists(paste0(address_prefix, "Heatmap.pdf")))
+
+# Test 4: Heatmap with FCcutoff also runs without error ----------------------
+expect_warning(
+    groupComparisonPlots(data = comparison_result, type = "Heatmap",
+                          FCcutoff = 70, logBase.pvalue = 2, address = address_prefix)
+)
+
+# Test 5: VolcanoPlot (ggplot2) creates a pdf file, no warning required ------
+invisible(capture.output(
+    groupComparisonPlots(data = comparison_result, type = "VolcanoPlot",
+                          logBase.pvalue = 2, address = address_prefix)
+))
+expect_true(file.exists(paste0(address_prefix, "VolcanoPlot.pdf")))
+
+# Test 6: VolcanoPlot with FCcutoff and no protein names ---------------------
+invisible(capture.output(
+    groupComparisonPlots(data = comparison_result, type = "VolcanoPlot",
+                          FCcutoff = 70, logBase.pvalue = 2, ylimUp = 100,
+                          ProteinName = FALSE, address = address_prefix)
+))
+
+# Test 7: ComparisonPlot (ggplot2) creates a pdf file and always warns -------
+expect_warning(
+    groupComparisonPlots(data = comparison_result, type = "ComparisonPlot",
+                          address = address_prefix)
+)
+expect_true(file.exists(paste0(address_prefix, "ComparisonPlot.pdf")))
+
+unlink(tmp_dir, recursive = TRUE)
+
+# plotly (isPlotly = TRUE) branches --------------------------------------------
+
+# Test 8: VolcanoPlot (plotly), address = FALSE, returns a list of plotly objects
+# (address = FALSE requires a single comparison to be selected)
+plotly_volcano = invisible(capture.output(
+    result_volcano <- groupComparisonPlots(data = comparison_result, type = "VolcanoPlot",
+                                            which.Comparison = "T3-T1",
+                                            logBase.pvalue = 2, address = FALSE,
+                                            isPlotly = TRUE)
+))
+expect_true(is.list(result_volcano))
+expect_true(length(result_volcano) > 0)
+expect_true(inherits(result_volcano[[1]], "plotly"))
+
+# Test 9: Heatmap (plotly), saved as a zipped HTML file ----------------------
+tmp_dir2 = tempfile("msstats_groupcomparisonplots_heatmap_")
+dir.create(tmp_dir2)
+address_prefix2 = paste0(tmp_dir2, "/")
+invisible(capture.output(suppressWarnings(
+    groupComparisonPlots(data = comparison_result, type = "Heatmap",
+                          logBase.pvalue = 2, address = address_prefix2,
+                          isPlotly = TRUE)
+)))
+expect_true(any(grepl("Heatmap.*\\.zip$", list.files(tmp_dir2))))
+unlink(tmp_dir2, recursive = TRUE)
+
+# Test 10: ComparisonPlot (plotly, all proteins), saved as a zipped HTML file
+tmp_dir3 = tempfile("msstats_groupcomparisonplots_comparison_")
+dir.create(tmp_dir3)
+address_prefix3 = paste0(tmp_dir3, "/")
+invisible(capture.output(suppressWarnings(
+    groupComparisonPlots(data = comparison_result, type = "ComparisonPlot",
+                          which.Protein = "all", address = address_prefix3,
+                          isPlotly = TRUE)
+)))
+expect_true(any(grepl("ComparisonPlot.*\\.zip$", list.files(tmp_dir3))))
+unlink(tmp_dir3, recursive = TRUE)