Merge pull request #125 from cbielow/mzqc_refact

Refactor to use rmzqc package
cbielow · Oct 14, 2022 · 83c0c3a · 83c0c3a
2 parents 1626c68 + c68309b
commit 83c0c3a
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Showing 35 changed files with 48 additions and 24,696 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -27,17 +27,16 @@ Imports:
     grDevices,
     gtable,
     htmlTable,
-    jsonlite,
     knitr (>= 1.10),
     magrittr,
     methods,
-    ontologyIndex,
     plyr,
     R6,
     R6P,
     RColorBrewer,
     reshape2,
     rmarkdown,
+    rmzqc (>= 0.3.0),
     seqinr,
     stats,
     utils,

diff --git a/NAMESPACE b/NAMESPACE
@@ -1,21 +1,9 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,PTXQC_table)
-export(CVDictionarySingleton)
 export(FilenameMapper)
 export(LCS)
 export(LCSn)
-export(MzQCDateTime)
-export(MzQCanalysisSoftware)
-export(MzQCbaseQuality)
-export(MzQCcontrolledVocabulary)
-export(MzQCcvParameter)
-export(MzQCinputFile)
-export(MzQCmetadata)
-export(MzQCmzQC)
-export(MzQCqualityMetric)
-export(NULL_to_NA)
-export(NULL_to_charNA)
 export(QCMetaFilenames)
 export(RTalignmentTree)
 export(YAMLClass)
@@ -29,8 +17,6 @@ export(createReport)
 export(createYaml)
 export(delLCP)
 export(delLCS)
-export(fromDatatoMzQC)
-export(getCVDictionary)
 export(getECDF)
 export(getFragmentErrors)
 export(getHTMLTable)
@@ -39,9 +25,6 @@ export(getMaxima)
 export(getPCA)
 export(getReportFilenames)
 export(grepv)
-export(hasFileSuffix)
-export(isUndefined)
-export(isValidMzQC)
 export(lcpCount)
 export(lcsCount)
 export(longestCommonPrefix)
@@ -86,21 +69,13 @@ export(qualLinThresh)
 export(qualMedianDist)
 export(qualUniform)
 export(read.MQ)
-export(removeSuffix)
 export(renameFile)
 export(repEach)
 export(shortenStrings)
 export(simplifyNames)
-export(suffixToCV)
 export(supCount)
 export(theme_blank)
 exportClasses(FilenameMapper)
-exportClasses(MzQCDateTime)
-exportClasses(MzQCanalysisSoftware)
-exportClasses(MzQCcontrolledVocabulary)
-exportClasses(MzQCcvParameter)
-exportClasses(MzQCinputFile)
-exportClasses(MzQCmetadata)
 exportClasses(YAMLClass)
 exportClasses(qcMetric)
 import(R6)
@@ -112,6 +87,7 @@ import(ggdendro)
 import(ggplot2)
 import(grDevices)
 import(grid)
+import(gridExtra)
 import(gtable)
 import(htmlTable)
 import(knitr)
@@ -120,6 +96,7 @@ import(methods)
 import(plyr)
 import(reshape2, except = c(dcast, melt))
 import(rmarkdown)
+import(rmzqc)
 import(stats)
 import(utils)
 import(xml2)

diff --git a/NEWS b/NEWS
@@ -8,15 +8,15 @@ Glossary:
  'issue' is an issue on GitHub
 
  The respective details can be found by visiting GitHub, e.g. https://github.com/cbielow/PTXQC/pull/124
- for pr #124 (you can use the same URL also for issues)
+ for pr #124 (you can use the same URL also for issues, just change the number)
 
 #################################
 #########   CHANGELOG  ##########
 #################################
 
 PRE!!! v1.00.15 -- 2022/??/??
   - better reporter ion minimum range in violin plot (pr #124)
-
+  - use 'rmzqc' package to handle mzQC output
 
 [CRAN] v1.00.14 -- 2022/09/21
   - [FIX] crash when re-running PTX-QC on a txt folder where a (very old) PTX-QC was already run (issue #118)

diff --git a/PTXQC.Rproj b/PTXQC.Rproj
@@ -0,0 +1,17 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source