[FIX] issue #25 (ambiguous MBR reference)

cbielow · Aug 2, 2016 · e37facc · e37facc
1 parent db18c12
commit e37facc
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: PTXQC
 Type: Package
 Title: Quality Report Generation for MaxQuant Results
-Version: 0.80.8
+Version: 0.80.9
 Date: 2016-02-15
 Author: Chris Bielow <chris.bielow@mdc-berlin.de>
 Maintainer: Chris Bielow <chris.bielow@mdc-berlin.de>

diff --git a/NEWS b/NEWS
@@ -5,6 +5,12 @@ i.e. a list of new features / bugfixes by version number.
 #########   CHANGELOG  ##########
 #################################
 
+v0.80.9 -- 2016/08/02
+  - bug fixes
+     - MBR-Metric: if more than one RT-reference is found (which can happen for a VERY stable LC), the first is picked
+       https://github.com/cbielow/PTXQC/issues/25
+  - minor doc improvements     
+
 v0.80.8 -- 2016/07/13
   - bug fixes
      - avoid crash in pre-calibration metric when there is only a single peptide identified in (any) Raw file

diff --git a/R/fcn_computeQC.R b/R/fcn_computeQC.R
@@ -362,7 +362,7 @@ createReport = function(txt_folder, yaml_obj = list())
       {
         ## fail hard; we could hack around this (e.g. by loading fasta headers from evidence.txt), but it wastes a lot of memory and time
         stop(paste0("Error: reporting of special contaminants requires loading of proteinGroups.txt.",
-                    "If you don't have this file, please disable contaminant lookup in the YAML file and re-run."))
+                    "If you don't have this file, please disable contaminant lookup in the YAML file ('SpecialContaminants: no') and re-run."))
       } else {
         lst_qcMetrics[["qcMetric_EVD_UserContaminant"]]$setData(d_evd, d_pg, yaml_contaminants)
       }

diff --git a/R/qcMetric_EVD.R b/R/qcMetric_EVD.R
@@ -466,9 +466,14 @@ Heatmap score [EVD: MBR Align]: fraction of 'green' vs. 'green+red' peptides.
       lpl = list()
       qcScore = .self$qcScores
 
-      if (length(refRaw) != 1) {
-        lpl[[1]] = ggText("EVD: Alignment check", paste0("Cannot find a unique reference Raw file (files: ", paste(refRaw, collapse=", "), ")"))
+      if (!evd_has_fractions && length(refRaw) == 0) {
+        lpl[[1]] = ggText("EVD: Alignment check", paste0("Cannot find a reference Raw file!\nPlease report this as a 'bug'!"))
       } else {
+        if (!evd_has_fractions & (length(refRaw) != 1))
+        {
+          refRaw = refRaw[1] ## take the first
+          warning(paste0("Cannot find a unique reference Raw file (files: ", paste(refRaw, collapse=", "), "). Picking the first."), immediate. = TRUE)
+        }
         ## find RT curve based on genuine 3D peaks (should be flat)
         d_alignQ = alignmentCheck(df_evd[(df_evd$type %in% c("MULTI-MSMS")), 
                                          c("calibrated.retention.time", 

diff --git a/R/qcMetric_PG.R b/R/qcMetric_PG.R
@@ -203,10 +203,13 @@ qcMetric_PG_PCA =  setRefClass(
     helpText = 
       "Principal components plots of experimental groups (as defined during MaxQuant configuration).
 
-This plot is shown only if more than one group was defined.
+This plot is shown only if more than one experimental group was defined.
 If LFQ was activated in MaxQuant, an additional PCA plot for LFQ intensities is shown. Similarly, if iTRAQ/TMT
 reporter intensities are detected.
 
+Since experimental groups and Raw files do not necessarily correspond 1:1, this plot cannot use the abbreviated
+Raw file names, but instead must rely on automatic shortening of group names.
+
 Heatmap score: none (since data source proteinGroups.txt is not related 1:1 to Raw files)
 ",
     workerFcn=function(.self, df_pg, lst_cols, MAP_pg_groups)