Move to a single report template

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

@@ -21,7 +21,7 @@ jobs:
         config:
         - { os: macOS-latest, bioc: 'release', curlConfigPath: '/usr/bin/'}
         - { os: windows-latest, bioc: 'release'}
-        - { os: ubuntu-latest, image: "bioconductor/bioconductor_docker:RELEASE_3_17", cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
+        - { os: ubuntu-latest, image: "bioconductor/bioconductor_docker:RELEASE_3_18", cran: "https://demo.rstudiopm.com/all/__linux__/xenial/latest"}
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
@@ -30,6 +30,7 @@ jobs:
       GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       CURL_CONFIG: ${{ matrix.config.curlConfigPath }}curl-config
+      cache-version: v1
 
     steps:
       - name: Check out repo
@@ -60,8 +61,8 @@ jobs:
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
-          restore-keys: ${{ runner.os }}-bioc-${{ matrix.config.bioc }}-
+          key: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ matrix.config.bioc }}-${{ hashFiles('depends.Rds') }}
+          restore-keys: ${{ env.cache-version }}-${{ runner.os }}-bioc-${{ matrix.config.bioc }}-
 
       - name: Install system dependencies (Linux)
         if: runner.os == 'Linux'

DESCRIPTION

@@ -1,13 +1,14 @@
 Package: einprot
 Type: Package
 Title: A collection of proteomics analysis utilities and workflows
-Version: 0.7.7
+Version: 0.9.4
 Authors@R: c(
     person("Charlotte", "Soneson", email = "charlotte.soneson@fmi.ch", 
            role = c("aut", "cre"), comment = c(ORCID = "0000-0003-3833-2169")),
     person("Jan", "Seebacher", role = "aut"),
     person("Michael", "Stadler", email = "michael.stadler@fmi.ch", 
            role = "aut", comment = c(ORCID = "0000-0002-2269-4934")),
+    person("Tobias", "Kockmann", role = "ctb"),
     person("Friedrich Miescher Institute for Biomedical Research", 
            role = c("cph")))
 Description: The einprot package contains utilities for performing analysis 
@@ -75,8 +76,9 @@ Imports:
     writexl,
     tools,
     grid,
-    ggseqlogo
-RoxygenNote: 7.2.3
+    Biostrings,
+    motifStack
+RoxygenNote: 7.3.1
 Suggests: 
     BiocManager,
     testthat (>= 3.0.0),

NAMESPACE

@@ -9,10 +9,12 @@ export(defineAssayNames)
 export(doImputation)
 export(doNormalization)
 export(doPCA)
+export(emptySampleText)
 export(expDesignText)
 export(filterFragPipe)
 export(filterMaxQuant)
 export(filterPDTMT)
+export(filterSpectronaut)
 export(fixFeatureIds)
 export(formatTableColumns)
 export(getCalibrationFrompdAnalysis)
@@ -33,7 +35,11 @@ export(getSupportedSpecies)
 export(getTemplateNamesFrompdAnalysis)
 export(getUniProtToIDMapping)
 export(getValidationInfoFrompdAnalysis)
+export(importDIANN)
 export(importExperiment)
+export(importSpectronaut)
+export(inputText)
+export(introText)
 export(listComplexDBs)
 export(makeAbundanceExport)
 export(makeAbundanceHeatmap)
@@ -53,20 +59,26 @@ export(plotMissingValuesHeatmap)
 export(plotVolcano)
 export(prepareFeatureCollections)
 export(prepareFinalSCE)
+export(readDIANNInfo)
 export(readFragPipeInfo)
 export(readMaxQuantXML)
 export(readProteomeDiscovererInfo)
+export(readSpectronautSetup)
+export(runDIANNAnalysis)
 export(runFragPipeAnalysis)
 export(runMaxQuantAnalysis)
 export(runPDTMTAnalysis)
 export(runPDTMTptmAnalysis)
 export(runPTMTest)
+export(runSpectronautAnalysis)
 export(runTest)
 export(saText)
 export(seqLogoApp)
 export(testText)
 import(STRINGdb)
 importFrom(BiocSingular,ExactParam)
+importFrom(Biostrings,AAStringSet)
+importFrom(Biostrings,consensusMatrix)
 importFrom(ComplexHeatmap,Heatmap)
 importFrom(ComplexHeatmap,columnAnnotation)
 importFrom(ComplexHeatmap,draw)
@@ -174,8 +186,6 @@ importFrom(ggplot2,theme)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,theme_minimal)
 importFrom(ggrepel,geom_text_repel)
-importFrom(ggseqlogo,ggseqlogo)
-importFrom(ggseqlogo,theme_logo)
 importFrom(grDevices,dev.off)
 importFrom(grDevices,hcl)
 importFrom(grDevices,pdf)
@@ -202,6 +212,8 @@ importFrom(limma,treat)
 importFrom(mclust,adjustedRandIndex)
 importFrom(methods,as)
 importFrom(methods,is)
+importFrom(motifStack,colorset)
+importFrom(motifStack,pcm2pfm)
 importFrom(msigdbr,msigdbr)
 importFrom(plotly,ggplotly)
 importFrom(proDA,proDA)
@@ -234,6 +246,8 @@ importFrom(stats,median)
 importFrom(stats,model.matrix)
 importFrom(stats,p.adjust)
 importFrom(stats,pt)
+importFrom(stats,quantile)
+importFrom(stats,rnorm)
 importFrom(stats,sd)
 importFrom(stats,setNames)
 importFrom(stringdist,amatch)
@@ -242,7 +256,10 @@ importFrom(tibble,rownames_to_column)
 importFrom(tidyr,gather)
 importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
+importFrom(tidyr,separate)
 importFrom(tidyr,separate_rows)
+importFrom(tidyr,separate_wider_delim)
+importFrom(tidyr,unite)
 importFrom(tidyr,unnest)
 importFrom(tidyselect,any_of)
 importFrom(tools,file_ext)

NEWS.md

@@ -1,3 +1,44 @@
+# einprot 0.9.4
+
+* Add details about DIA-NN command line to report
+* Add column with links to ComplexPortal query to link table
+* Include pathways from MSigDB among supported feature collections
+* Update DIA-NN example data
+* Expand input data paths in run*Analysis() functions
+* Add support for importing Spectronaut PG pivot files
+* Add initial support for reading Spectronaut setup.txt files
+
+# einprot 0.9.3
+
+* Significantly expand the built-in complex database by adding complexes from the Complex Portal and hu.MAP 2.0
+* Hide box plot legends if there are too many groups
+* Add MinProbGlobal imputation method
+* Add makeInteractiveVolcano argument to plotVolcano
+
+# einprot 0.9.2
+
+* Fix sample column name in DIA-NN import
+* Adapt DIA-NN log import to handle vector output
+* Add argument addHeatmaps to run functions, to allow suppression of heatmaps for large data sets
+* Remove samples with no detected features
+* Add support for Spectronaut protein group output
+* Add support for displayName column in sample annotation table
+* Add extraFeatureCols argument for specification of user-defined feature annotation columns
+* Extract information about Top N ions for FragPipe
+
+# einprot 0.9.1
+
+* Replace ggseqlogo dependency with motifStack
+* Adapt missing value plots to work with both proportions and percentages
+
+# einprot 0.9.0
+
+* Consolidate tool-specific templates into a single template
+
+# einprot 0.8.0
+
+* Add support for DIA-NN protein group data
+
 # einprot 0.7.7
 
 * Change default value of singleFit to TRUE everywhere, for consistency

R/addSampleAnnots.R

@@ -63,5 +63,15 @@ addSampleAnnots <- function(sce, sampleAnnot) {
             sampleAnnot[[cn]][match(sce$sample, sampleAnnot$sample)]
     }
 
+    if ("displayName" %in% colnames(sampleAnnot)) {
+        if (any(duplicated(sampleAnnot$displayName))) {
+            stop("'displayName' column contains duplicated values")
+        }
+        colnames(sce) <- rownames(SummarizedExperiment::colData(sce)) <-
+            sce$displayName
+        sce$originalSample <- sce$sample
+        sce$sample <- sce$displayName
+    }
+
     sce
 }