Merge pull request #4 from fmicompbio/devel-jul

developments

.github/workflows/R-CMD-check.yaml

@@ -19,7 +19,7 @@ jobs:
         config:
         - { os: macOS-latest, bioc: 'release', curlConfigPath: '/usr/bin/'}
         - { os: windows-latest, bioc: 'release'}
-        - { os: ubuntu-latest, image: "bioconductor/bioconductor_docker:RELEASE_3_15", cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+        - { os: ubuntu-latest, image: "bioconductor/bioconductor_docker:RELEASE_3_16", cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -40,7 +40,7 @@ jobs:
           bioc-version: ${{ matrix.config.bioc }}
 
       - name: Set up pandoc
-        uses: r-lib/actions/setup-pandoc@master
+        uses: r-lib/actions/setup-pandoc@v2
         if: matrix.config.image == null
 
       - name: Install remotes

DESCRIPTION

@@ -1,11 +1,10 @@
 Package: einprot
 Type: Package
-Title: A one-stop shop for proteomics analysis utilities
-Version: 0.5.13
+Title: A collection of proteomics analysis utilities and workflows
+Version: 0.6.5
 Authors@R: c(
     person("Charlotte", "Soneson", email = "[email protected]", 
-           role = c("aut", "cre"),
-           comment = c(ORCID = "0000-0003-3833-2169")),
+           role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3833-2169")),
     person("Jan", "Seebacher", role = "aut"),
     person("Michael", "Stadler", email = "[email protected]", 
            role = "aut", comment = c(ORCID = "0000-0002-2269-4934")),
@@ -21,21 +20,18 @@ LazyData: false
 Depends: R (>= 4.0)
 Imports: 
     babelgene,
-    BiocSingular,
     circlize,
     ComplexHeatmap,
     cowplot,
     dplyr,
     DT,
     genefilter,
     ggiraph,
-    ggplot2,
+    ggplot2 (>= 3.4.0),
     grDevices,
     ggrepel,
-    GSEABase,
     imputeLCMD,
     IRanges,
-    iSEE,
     iSEEu,
     kableExtra,
     limma,
@@ -60,17 +56,24 @@ Imports:
     tibble,
     tidyr,
     utils,
-    vsn,
     xfun,
     XML,
     xml2,
     ExploreModelMatrix,
     ComplexUpset,
     htmltools,
-    knitr
-RoxygenNote: 7.2.0
+    knitr,
+    proDA,
+    forcats,
+    ggalt,
+    BiocSingular,
+    tidyselect,
+    GGally,
+    scuttle
+RoxygenNote: 7.2.3
 Suggests: 
     BiocManager,
-    testthat (>= 3.0.0)
+    testthat (>= 3.0.0),
+    iSEE
 Config/testthat/edition: 3
 VignetteBuilder: knitr

NAMESPACE

@@ -4,13 +4,20 @@ export(EINPROT_COMPLEXES_FILE)
 export(EINPROT_POMBASE_CONVTABLE)
 export(EINPROT_WORMBASE_CONVTABLE)
 export(addSampleAnnots)
+export(combineIds)
+export(defineAssayNames)
 export(doImputation)
+export(doNormalization)
+export(doPCA)
 export(expDesignText)
+export(filterMaxQuant)
+export(filterPDTMT)
 export(fixFeatureIds)
 export(getCalibrationFrompdAnalysis)
 export(getColumnNames)
 export(getContaminantsDatabaseFrompdAnalysis)
 export(getConvTable)
+export(getFirstId)
 export(getIntensityColumns)
 export(getMatSubtractedBaseline)
 export(getPSMValidationInfoFrompdAnalysis)
@@ -20,6 +27,7 @@ export(getSearchParametersFrompdAnalysis)
 export(getSpeciesInfo)
 export(getSupportedSpecies)
 export(getTemplateNamesFrompdAnalysis)
+export(getUniProtToIDMapping)
 export(getValidationInfoFrompdAnalysis)
 export(importExperiment)
 export(listComplexDBs)
@@ -28,6 +36,7 @@ export(makeDbLinkTable)
 export(makeIntensityBoxplots)
 export(makeListOfComparisons)
 export(makeMeanSDPlot)
+export(makeSAPlot)
 export(makeTableFromList)
 export(makeiSEEScript)
 export(normText)
@@ -39,38 +48,35 @@ export(plotPDTMTqc)
 export(plotVolcano)
 export(prepareFeatureCollections)
 export(prepareFinalSCE)
-export(readFragPipeInfo)
 export(readMaxQuantXML)
 export(readProteomeDiscovererInfo)
-export(runFragPipeAnalysis)
 export(runMaxQuantAnalysis)
 export(runPDTMTAnalysis)
+export(runPDTMTptmAnalysis)
+export(runPTMTest)
 export(runTest)
 export(saText)
 export(testText)
-import(ComplexHeatmap)
-import(ComplexUpset)
-import(DT)
-import(ExploreModelMatrix)
-import(QFeatures)
 import(STRINGdb)
-import(SummarizedExperiment)
-import(dplyr)
-import(ggplot2)
-import(htmltools)
-import(knitr)
-import(scater)
+importFrom(BiocSingular,ExactParam)
 importFrom(ComplexHeatmap,Heatmap)
+importFrom(ComplexHeatmap,columnAnnotation)
+importFrom(ComplexHeatmap,draw)
+importFrom(ComplexUpset,upset)
+importFrom(DT,datatable)
+importFrom(ExploreModelMatrix,VisualizeDesign)
+importFrom(GGally,ggpairs)
 importFrom(IRanges,CharacterList)
 importFrom(MsCoreUtils,impute_matrix)
 importFrom(MsCoreUtils,normalizeMethods)
-importFrom(MsCoreUtils,normalize_matrix)
 importFrom(QFeatures,readSummarizedExperiment)
 importFrom(S4Vectors,DataFrame)
+importFrom(S4Vectors,combineCols)
 importFrom(S4Vectors,endoapply)
 importFrom(S4Vectors,mcols)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SingleCellExperiment,reducedDim)
 importFrom(SummarizedExperiment,"assay<-")
 importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,assay)
@@ -85,39 +91,53 @@ importFrom(cowplot,plot_grid)
 importFrom(cowplot,theme_cowplot)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,across)
+importFrom(dplyr,all_of)
 importFrom(dplyr,arrange)
 importFrom(dplyr,between)
+importFrom(dplyr,bind_cols)
 importFrom(dplyr,bind_rows)
 importFrom(dplyr,case_when)
 importFrom(dplyr,contains)
 importFrom(dplyr,desc)
 importFrom(dplyr,distinct)
 importFrom(dplyr,everything)
 importFrom(dplyr,filter)
+importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
+importFrom(dplyr,last_col)
 importFrom(dplyr,left_join)
 importFrom(dplyr,matches)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)
+importFrom(dplyr,relocate)
 importFrom(dplyr,rename)
 importFrom(dplyr,row_number)
 importFrom(dplyr,select)
+importFrom(dplyr,slice)
 importFrom(dplyr,slice_head)
+importFrom(dplyr,starts_with)
 importFrom(dplyr,summarize)
 importFrom(dplyr,tally)
 importFrom(dplyr,ungroup)
+importFrom(forcats,fct_reorder)
 importFrom(genefilter,rowSds)
 importFrom(genefilter,rowttests)
+importFrom(ggalt,geom_encircle)
 importFrom(ggiraph,geom_point_interactive)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,after_stat)
 importFrom(ggplot2,annotate)
 importFrom(ggplot2,coord_cartesian)
+importFrom(ggplot2,coord_fixed)
+importFrom(ggplot2,coord_flip)
 importFrom(ggplot2,element_blank)
+importFrom(ggplot2,element_line)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expand_limits)
 importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_boxplot)
+importFrom(ggplot2,geom_col)
 importFrom(ggplot2,geom_errorbar)
 importFrom(ggplot2,geom_histogram)
 importFrom(ggplot2,geom_hline)
@@ -129,12 +149,16 @@ importFrom(ggplot2,geom_smooth)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_vline)
 importFrom(ggplot2,ggplot)
+importFrom(ggplot2,ggtitle)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,layer_data)
 importFrom(ggplot2,position_dodge)
 importFrom(ggplot2,rel)
 importFrom(ggplot2,scale_fill_continuous)
+importFrom(ggplot2,scale_fill_gradient2)
 importFrom(ggplot2,scale_fill_manual)
+importFrom(ggplot2,scale_x_continuous)
+importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,scale_y_log10)
 importFrom(ggplot2,stat_density2d)
 importFrom(ggplot2,theme)
@@ -143,24 +167,32 @@ importFrom(ggplot2,theme_minimal)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,pdf)
+importFrom(htmltools,tagList)
 importFrom(iSEEu,registerAveAbFields)
 importFrom(iSEEu,registerFeatureSetCollections)
 importFrom(iSEEu,registerLogFCFields)
 importFrom(iSEEu,registerPValueFields)
+importFrom(imputeLCMD,impute.MinProb)
 importFrom(kableExtra,column_spec)
 importFrom(kableExtra,kable_paper)
 importFrom(kableExtra,kbl)
+importFrom(knitr,current_input)
 importFrom(limma,cameraPR)
+importFrom(limma,contrasts.fit)
+importFrom(limma,eBayes)
 importFrom(limma,ids2indices)
 importFrom(limma,lmFit)
 importFrom(limma,removeBatchEffect)
+importFrom(limma,topTable)
 importFrom(limma,topTreat)
 importFrom(limma,treat)
 importFrom(mclust,adjustedRandIndex)
 importFrom(methods,as)
 importFrom(methods,is)
 importFrom(msigdbr,msigdbr)
 importFrom(plotly,ggplotly)
+importFrom(proDA,proDA)
+importFrom(proDA,test_diff)
 importFrom(readr,read_file)
 importFrom(readr,read_tsv)
 importFrom(readr,write_file)
@@ -169,7 +201,11 @@ importFrom(rmarkdown,pandoc_available)
 importFrom(rmarkdown,pandoc_exec)
 importFrom(rmarkdown,render)
 importFrom(rrcovNA,impSeqRob)
+importFrom(scales,muted)
 importFrom(scales,percent)
+importFrom(scales,percent_format)
+importFrom(scater,runPCA)
+importFrom(scuttle,makePerCellDF)
 importFrom(stats,median)
 importFrom(stats,model.matrix)
 importFrom(stats,p.adjust)
@@ -184,10 +220,15 @@ importFrom(tidyr,gather)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,separate_rows)
 importFrom(tidyr,unnest)
+importFrom(tidyselect,any_of)
 importFrom(utils,combn)
 importFrom(utils,download.file)
+importFrom(utils,head)
 importFrom(utils,packageVersion)
+importFrom(utils,read.csv)
 importFrom(utils,read.delim)
+importFrom(utils,stack)
+importFrom(utils,tail)
 importFrom(utils,unzip)
 importFrom(utils,write.table)
 importFrom(xfun,Rscript_call)

NEWS.md

@@ -1,3 +1,82 @@
+# einprot 0.6.5
+
+* Change correlation heatmap appearance
+* Provide the possibility to run the workflows without statistical tests
+* Allow specifying the iColPattern without escaped periods
+
+# einprot 0.6.4
+
+* Include test results and comparison list in returned SummarizedExperiment
+* Expand the PCA plots with scree plots and coefficient plots
+* Add option to label any/only significant features in volcano plot
+* Add einprotLabel column to link table
+
+# einprot 0.6.3
+
+* Combine PTM tests into a single function
+
+# einprot 0.6.2
+
+* Lift out PTM tests into separate functions
+* Change interface to defining protein ID column in PTM workflow
+* Add tour to iSEE script
+
+# einprot 0.6.1
+
+* Use only spike features with no missing values for normalization
+* Add stringIdCol argument
+* Lift out filtering and SA plots into separate functions
+
+# einprot 0.6.0
+
+* Change handling of feature identifiers - new arguments idCol, labelCol
+
+# einprot 0.5.22
+
+* Check STRING connection, skip STRING analysis in case of problems
+
+# einprot 0.5.21
+
+* Add idCol argument to PD-TMT workflow
+
+# einprot 0.5.20
+
+* Add samSignificance argument to runTest
+
+# einprot 0.5.19
+
+* Bugfix in PTM workflow to correctly access comparisons
+* Add function to map UniProtIDs to gene symbols
+* Include STRING networks also for PD-TMT workflow
+* Allow t-test for PD-TMT workflow
+
+# einprot 0.5.18
+
+* Allow also Abundances.grouped for PD data
+
+# einprot 0.5.17
+
+* Allow custom names of comparisons
+
+# einprot 0.5.16
+
+* Show only features that are significant in at least one comparison in upset plot
+* Expand capabilities of test (a group can belong to more than one merged group, a group can be tested against its complement)
+
+# einprot 0.5.15
+
+* Move normalization to a separate function
+* Allow estimating normalization factors from spike features
+* Move normalization before imputation
+
+# einprot 0.5.14
+
+* Use eBayes rather than treat if minlFC = 0
+* Allow using proDA for differential abundance testing
+* Allow the user to specify which PD quantification file to use
+* Allow running PD workflow without pdAnalysis file
+* Add first version of PD-TMT PTM workflow
+
 # einprot 0.5.13
 
 * Update readFragPipeInfo to use log file instead of config file