Filtering of missing values now in quantable instead of Grp2Analysis.R

protViz · Nov 26, 2018 · 96767d9 · 96767d9
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commit 96767d9
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/R/Grp2Analysis.R b/R/Grp2Analysis.R
@@ -283,7 +283,7 @@ Grp2Analysis <- setRefClass("Grp2Analysis",
 
                                 # Retrieve normalized data for clustering
                                 tmpdata1 <- .self$getNormalized()$data
-                                tmpdata1 <- tmpdata1[.self$getNrNAs() < ncol(tmpdata1)/2,]
+
                                 # Clustering using quantable::simpleheatmap3()
                                 clustering <- quantable::simpleheatmap3(t(tmpdata1), margins=c(1,10),
                                                                         breaks = seq(-2.5,2.5, length=26),

diff --git a/inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R b/inst/RunScripts/Run_Generic_QuantTwoGroupAnalysis.R
@@ -99,4 +99,4 @@ genericQuantMatrixGRP2 <- grp2
 ## REMOVE TO RENDER
 #rmarkdown::render("vignettes/Grp2Analysis.Rmd", params = list(grp = genericQuantMatrixGRP2), envir = new.env())
 
-
+rmarkdown::render("vignettes/Grp2AnalysisHeatmap3.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))
Original file line number	Diff line number	Diff line change
Expand Up		@@ -99,4 +99,4 @@ genericQuantMatrixGRP2 <- grp2
		## REMOVE TO RENDER
		#rmarkdown::render("vignettes/Grp2Analysis.Rmd", params = list(grp = genericQuantMatrixGRP2), envir = new.env())


		rmarkdown::render("vignettes/Grp2AnalysisHeatmap3.Rmd",bookdown::pdf_document2(), params=list(grp = grp2))