@@ -1,6 +1,6 @@

 Package: limma

-Version: 3.41.4

-Date: 2019-06-16

+Version: 3.41.5

+Date: 2019-06-17

 Title: Linear Models for Microarray Data

 Description: Data analysis, linear models and differential expression for microarray data.

 Author: Gordon Smyth [cre,aut], Yifang Hu [ctb], Matthew Ritchie [ctb], Jeremy Silver [ctb], James Wettenhall [ctb], Davis McCarthy [ctb], Di Wu [ctb], Wei Shi [ctb], Belinda Phipson [ctb], Aaron Lun [ctb], Natalie Thorne [ctb], Alicia Oshlack [ctb], Carolyn de Graaf [ctb], Yunshun Chen [ctb], Mette Langaas [ctb], Egil Ferkingstad [ctb], Marcus Davy [ctb], Francois Pepin [ctb], Dongseok Choi [ctb]

@@ -130,3 +130,4 @@ S3method(plotDensities,RGList)

 S3method(plotDensities,MAList)

 S3method(plotDensities,EListRaw)

 S3method(plotDensities,EList)

+S3method(unique,TestResults)

@@ -249,3 +249,5 @@ as.data.frame.MArrayLM <- function(x, row.names = NULL, optional = FALSE, ...)

 	if(ncoef==1) x <- lapply(x,drop)

 	as.data.frame(x,row.names=row.names,optional=optional)

 }

+

+unique.TestResults <- function(x,...) unique([email protected],...)

@@ -30,7 +30,7 @@ plotMD.MAList <- function(object, column=1, array=NULL, xlab="A", ylab="M", main

 plotMD.MArrayLM <- function(object, column=ncol(object), coef=NULL, xlab="Average log-expression", ylab="log-fold-change", main=colnames(object)[column], status=object$genes$Status, zero.weights=FALSE, ...)

 #	Mean-difference plot with color coding for controls

 #	Gordon Smyth 7 April 2003, James Wettenhall 27 June 2003.

-#	Last modified 16 June 2019.

+#	Last modified 17 June 2019.

 {

 	if(!is.null(coef)) column <- coef

 	if(is.null(object$Amean)) stop("Amean component is absent.")

@@ -39,19 +39,12 @@ plotMD.MArrayLM <- function(object, column=ncol(object), coef=NULL, xlab="Averag

 		w <- as.matrix(object$weights)[,column]

 		logFC[ is.na(w) | (w <= 0) ] <- NA

 	}

-	if(is(status,"TestResults")) {

-		if(ncol(status) > 1L) status <- status[,column]

-		Dots <- list(...)

-#		Set values and colors only if 'values' is not already specified as an argument

-		if(is.null(Dots$values)) {

-			f <- factor([email protected],levels=c(-1,0,1))

-			levels(f) <- attr(status,"labels")

-			f <- as.character(f)

-			attr(f,"values") <- c("Up","Down")

-			attr(f,"col") <- c("red","blue")

-			status <- f

-		}

-	}

+	if(is(status,"TestResults"))

+		if(ncol(status) > 1L)

+			if(ncol(status == ncol(object)))

+				status <- status[,column]

+			else

+				stop("status has multiple columns")

 	plotWithHighlights(x=object$Amean,y=logFC,xlab=xlab,ylab=ylab,main=main,status=status,...)

 }

@@ -5,7 +5,7 @@ plotWithHighlights <- function(x, y, status=NULL, values=NULL, hl.pch=16, hl.col

 #	created by Gordon Smyth 7 April 2003 and modified by James Wettenhall 27 June 2003.

 #	Gordon Smyth

-#	Last modified 27 May 2017.

+#	Last modified 17 June 2019.

 {

 #	If no status information, just plot all points normally

 	if(is.null(status) || all(is.na(status))) {

@@ -18,10 +18,22 @@ plotWithHighlights <- function(x, y, status=NULL, values=NULL, hl.pch=16, hl.col

 #	Check values

 	if(is.null(values)) {

 		if(is.null(attr(status,"values"))) {

-#			Default is to set the most frequent status value as background, and to highlight other status values in decreasing order of frequency

-			status.values <- names(sort(table(status),decreasing=TRUE))

-			status <- as.character(status)

-			values <- status.values[-1]

+			if(is(status,"TestResults")) {

+				if(ncol(status) > 1L) stop("status has more than one column")

+				Values <- c(-1L,0L,1L)

+				Labels <- c("Down","NotSig","Up")

+				f <- factor([email protected],levels=Values)

+				levels(f) <- Labels

+				status <- as.character(f)

+				values <- c("Up","Down")

+				if(is.null(hl.col)) hl.col <- c("red","blue")

+			} else {

+#				Default is to set the most frequent status value as background,

+#				and to highlight other status values in decreasing order of frequency

+				status.values <- names(sort(table(status),decreasing=TRUE))

+				status <- as.character(status)

+				values <- status.values[-1]

+			}

 		} else {

 #			Use values and graphics parameters set as attributes by controlStatus()

 			values <- attr(status,"values")

@@ -1,11 +1,13 @@

-16 June 2019: limma 3.41.5

+17 June 2019: limma 3.41.5

-- plotMD.MArrayLM now gives special treatment to the case that

-  `status` is a TestResults object.

+- plotWithHighlights and plotMD.MArrayLM now gives special treatment

+  to the case that `status` is a TestResults object.

+

+- new S3 unique() method for TestResults objects.

 16 June 2019: limma 3.41.4

-- New subsetting method for TestResults objects. Previously a

+- New S3 subsetting method for TestResults objects. Previously a

   subsetted TestResults object became an ordinary numeric matrix, but

   now the TestResults class is preserved. Single index subsetting is

   also allowed but produces a numeric vector.

@@ -5,6 +5,7 @@

 \alias{summary.TestResults}

 \alias{levels.TestResults}

 \alias{labels.TestResults}

+\alias{unique.TestResults}

 \title{Matrix of Test Results - class}

 \description{

@@ -14,12 +14,16 @@ plotWithHighlights(x, y, status = NULL, values = NULL,

 \arguments{

   \item{x}{numeric vector.}

-  \item{y}{numeric vector.}

+  \item{y}{numeric vector of same length as \code{x}.}

-  \item{status}{character vector giving the control status of each point, of same length as \code{x} and \code{y}.

-  If \code{NULL}, then all points are plotted in the background color, symbol and size.}

+  \item{status}{

+    character vector giving the control status of each point, of same length as \code{x} and \code{y},

+    or else a \code{TestResults} object with one column and number of rows matching the length of \code{x}.

+    If \code{NULL}, then all points are plotted in the background color, symbol and size.

+  }

   \item{values}{character vector giving values of \code{status} to be highlighted on the plot.

+  Set automatically if \code{status} contains \code{TestResults}.

   Defaults to unique values of \code{status} in decreasing order of frequency, with the most frequent value set as the background value.

   Ignored if there is no \code{status} vector.}

@@ -27,6 +31,7 @@ plotWithHighlights(x, y, status = NULL, values = NULL,

   Ignored is there is no \code{status} vector.}

   \item{hl.col}{vector of colors for highlighted points, either of unit length or of same length as \code{values}.

+  Set automatically if \code{status} contains \code{TestResults}.

   Defaults to \code{1+1:length(values)}.

   Ignored if there is no \code{status} vector.}