v2.0.0 (2020-04-01). Result classes; refactor plots to all use ggplot2

.travis.yml

@@ -13,6 +13,8 @@ cache:
 #branches:
 #  only:
 #    - master
+before_install:
+  - sudo apt-get -y install libmagick++-dev
 
 r_github_packages:
   - jimhester/covr
@@ -25,4 +27,4 @@ notifications:
     on_failure: always # default: always
 
 after_success:
-  - Rscript -e 'library(covr);codecov()'
+  - Rscript -e 'library(covr); codecov()'

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: BASiCS
 Type: Package
 Title: Bayesian Analysis of Single-Cell Sequencing data
-Version: 1.9.26
-Date: 2020-03-25
+Version: 2.0.0
+Date: 2020-04-01
 Authors@R: c(person("Catalina", "Vallejos", role=c("aut", "cre"),
         email="[email protected]"), 
         person("Nils", "Eling", role=c("aut")), 
@@ -34,6 +34,7 @@ Description: Single-cell mRNA sequencing can uncover novel cell-to-cell
     mean/over-dispersion trend. 
 License: GPL (>= 2)
 Depends:
+    R (>= 3.6.0),
     SingleCellExperiment
 Imports:
     Biobase,
@@ -57,12 +58,15 @@ Imports:
     utils,
     Matrix,
     matrixStats,
-    assertthat
+    assertthat,
+    reshape2,
+    hexbin
 Suggests:
     BiocStyle,
     knitr,
     rmarkdown,
-    testthat
+    testthat,
+    magick
 LinkingTo: Rcpp, RcppArmadillo
 VignetteBuilder: knitr
 biocViews: ImmunoOncology, Normalization, Sequencing, RNASeq, Software, 
@@ -72,10 +76,11 @@ SystemRequirements: C++11
 NeedsCompilation: yes
 URL: https://github.com/catavallejos/BASiCS
 BugReports: https://github.com/catavallejos/BASiCS/issues
-RoxygenNote: 7.0.2
+RoxygenNote: 7.1.0
 Encoding: UTF-8
 LazyData: true
 Collate: 
+    'AllClasses.R'
     'AllGenerics.R'
     'BASiCS_CorrectOffset.R'
     'BASiCS_DenoisedCounts.R'
@@ -89,18 +94,17 @@ Collate:
     'BASiCS_LoadChain.R'
     'BASiCS_MCMC.R'
     'BASiCS_Package.R'
+    'BASiCS_PlotDE.R'
+    'BASiCS_PlotOffset.R'
     'BASiCS_PriorParam.R'
     'BASiCS_ShowFit.R'
     'BASiCS_Sim.R'
     'BASiCS_TestDE.R'
     'BASiCS_VarThresholdSearchHVG_LVG.R'
     'BASiCS_VarianceDecomp.R'
-    'Classes.R'
     'HiddenBASiCS_Sim.R'
     'HiddenHeaderBASiCS_Sim.R'
-    'HiddenHeaderDetectHVG_LVG.R'
     'HiddenHeaderTest_DE.R'
-    'HiddenPlotsDetectHVG_LVG.R'
     'HiddenVarDecomp.R'
     'utils_Misc.R'
     'Methods.R'

NAMESPACE

@@ -5,46 +5,54 @@ export(BASiCS_DenoisedCounts)
 export(BASiCS_DenoisedRates)
 export(BASiCS_DetectHVG)
 export(BASiCS_DetectLVG)
+export(BASiCS_DetectVG)
 export(BASiCS_DiagHist)
 export(BASiCS_DiagPlot)
 export(BASiCS_Draw)
 export(BASiCS_EffectiveSize)
 export(BASiCS_Filter)
 export(BASiCS_LoadChain)
 export(BASiCS_MCMC)
+export(BASiCS_PlotDE)
+export(BASiCS_PlotOffset)
+export(BASiCS_PlotVG)
 export(BASiCS_PriorParam)
 export(BASiCS_ShowFit)
 export(BASiCS_Sim)
 export(BASiCS_TestDE)
 export(BASiCS_VarThresholdSearchHVG)
 export(BASiCS_VarThresholdSearchLVG)
+export(BASiCS_VarThresholdSearchVG)
 export(BASiCS_VarianceDecomp)
 export(BASiCS_diagHist)
 export(BASiCS_diagPlot)
 export(BASiCS_effectiveSize)
 export(BASiCS_showFit)
+export(displayChainBASiCS)
+export(displaySummaryBASiCS)
 export(makeExampleBASiCS_Data)
 export(newBASiCS_Chain)
 export(newBASiCS_Data)
 exportClasses(BASiCS_Chain)
 exportClasses(BASiCS_Summary)
+exportMethods("[")
+exportMethods("[[")
+exportMethods("rowData<-")
+exportMethods(BASiCS_PlotDE)
 exportMethods(Summary)
 exportMethods(dim)
 exportMethods(dimnames)
 exportMethods(displayChainBASiCS)
 exportMethods(displaySummaryBASiCS)
+exportMethods(format)
 exportMethods(plot)
+exportMethods(rowData)
 exportMethods(show)
 exportMethods(subset)
 exportMethods(updateObject)
 importClassesFrom(Biobase,Versioned)
 importFrom(KernSmooth,bkde2D)
 importFrom(MASS,mvrnorm)
-importFrom(Matrix,colMeans)
-importFrom(Matrix,colSums)
-importFrom(Matrix,rowMeans)
-importFrom(Matrix,rowSums)
-importFrom(Matrix,t)
 importFrom(Rcpp,evalCpp)
 importFrom(S4Vectors,"metadata<-")
 importFrom(S4Vectors,DataFrame)
@@ -56,11 +64,13 @@ importFrom(SingleCellExperiment,altExp)
 importFrom(SingleCellExperiment,altExpNames)
 importFrom(SingleCellExperiment,counts)
 importFrom(SummarizedExperiment,"colData<-")
+importFrom(SummarizedExperiment,"rowData<-")
 importFrom(SummarizedExperiment,SummarizedExperiment)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,assayNames)
 importFrom(SummarizedExperiment,assays)
 importFrom(SummarizedExperiment,colData)
+importFrom(SummarizedExperiment,rowData)
 importFrom(assertthat,assert_that)
 importFrom(coda,HPDinterval)
 importFrom(coda,effectiveSize)
@@ -97,11 +107,13 @@ importFrom(graphics,par)
 importFrom(graphics,points)
 importFrom(graphics,segments)
 importFrom(graphics,smoothScatter)
+importFrom(hexbin,hexbin)
 importFrom(matrixStats,colMeans2)
 importFrom(matrixStats,colMedians)
 importFrom(matrixStats,colVars)
 importFrom(matrixStats,rowMeans2)
 importFrom(matrixStats,rowMedians)
+importFrom(matrixStats,rowVars)
 importFrom(methods,.hasSlot)
 importFrom(methods,Summary)
 importFrom(methods,is)
@@ -129,4 +141,6 @@ importMethodsFrom(BiocGenerics,counts)
 importMethodsFrom(BiocGenerics,rownames)
 importMethodsFrom(BiocGenerics,subset)
 importMethodsFrom(BiocGenerics,updateObject)
+importMethodsFrom(Matrix,rowMeans)
+importMethodsFrom(Matrix,t)
 useDynLib(BASiCS)

NEWS

@@ -1433,3 +1433,10 @@ version 1.9.25 (2020-03-13)
 version 1.9.26 (2020-03-25)
 - Bugfix in BASiCS_Sim
 
+version 2.0.0 (2020-04-01)
+- Improve UI for BASiCS_TestDE BASiCS_TestHVG/BASiCS_TestLVG and related 
+  functions by creating classes. Usage of objects documented in vignette.
+- Reduce code duplication and refactor plots to use ggplot2. 
+- Add rudimentary unit tests for loading and some class methods.
+  Fix several minor bugs.
+- Change barplot in variance decomposition function to use ggplot2.