cleanup

protViz · Aug 13, 2019 · 624fa5f · 624fa5f
1 parent 445a561
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -11,11 +11,11 @@ Author: Witold Wolski
 Description: Analysing and LFQ and SRM experiments in service mode.
     Data preprocessing and visualization.
 Imports:
-    bibliospec,
     bookdown,
     conflicted,
     corrplot,
     dplyr,
+    forcats,
     glue,
     gridExtra,
     heatmap3,

diff --git a/R/Grp2Analysis.R b/R/Grp2Analysis.R
@@ -168,14 +168,16 @@ Grp2Analysis <- setRefClass("Grp2Analysis",
                                 fileID <- as.character(subset(.self$annotation_, Condition == condition)$Raw.file)
                                 normalized[, fileID]
                               },
+                              resetModelMatrix = function(){
+                                .self$modelMatrix <- matrix(ncol=0, nrow=0)
+                              },
                               setModelMatrix = function(modelMatrix){
                                 .self$modelMatrix <- modelMatrix
                               },
                               getDesignMatrix = function(){
                                 if(isTRUE(all.equal(dim(.self$modelMatrix), c(0,0)))){
                                   # hack for putting reference into denomintor.
-                                  design <- gsub(reference, paste("A_", reference, sep=""),
-                                                 .self$annotation_$Condition)
+                                  design <- forcats::fct_relevel(.self$annotation_$Condition, .self$reference)
                                   .self$modelMatrix <- model.matrix(~design)
                                 }
                                 return(.self$modelMatrix)

diff --git a/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R b/inst/RunScripts/Run_MQ_QuantTwoGroupAnalysis.R
@@ -60,11 +60,14 @@ grp2 <- Grp2Analysis(annotation, "Experimentname",
                      numberOfProteinClusters = 20
                      )
 
+grp2$getDesignMatrix()
+
 grp2$setMQProteinGroups(protein)
 grp2$setQValueThresholds(qvalue = qvalueThreshold,qfoldchange = qfoldchange)
 mqQuantMatrixGRP2 <- grp2
 
 head(mqQuantMatrixGRP2$getModPValuesCI())
+
 usethis::use_data(mqQuantMatrixGRP2, overwrite = TRUE)
 #readr::write_tsv(grp2$getResultTable(), path=file.path(resultdir,"pValues.csv"))
 

diff --git a/inst/samples/plotlyExample.Rmd b/inst/samples/plotlyExample.Rmd
diff --git a/inst/samples/plotlyViewer/ProteinPeptideViewer.Rmd b/inst/samples/plotlyViewer/ProteinPeptideViewer.Rmd
diff --git a/inst/samples/plotlyViewer/RenderPepideProteinViewer.R b/inst/samples/plotlyViewer/RenderPepideProteinViewer.R
diff --git a/vignettes/Grp2PullDownExample.Rmd b/vignettes/Grp2PullDownExample.Rmd
@@ -16,7 +16,7 @@ header-includes:
 params:
   grp: !r quote(SRMService::grp2PullDownExample)
 vignette: >
-  %\VignetteIndexEntry{FGCZ Two-Group Analysis}
+  %\VignetteIndexEntry{FGCZ Two-Group Analysis - pull down example}
   %\VignetteEncoding{UTF-8}
   %\VignetteEngine{knitr::rmarkdown}
 bibliography: bibliography.bib