@@ -1,33 +1,38 @@

-#' Function for biplotting with no point labels and with points color-coded according 

-#' to a quantitative variable. For example: the rank of normalization performance.

-#'

+#' Function for biplotting with no point labels and with

+#' points color-coded according to a quantitative variable.

+#' For example: the rank of normalization performance.

+#' 

 #' This function implements biplot for \code{\link[stats]{prcomp}} objects.

-#'

+#' 

 #' @param x \code{\link[stats]{prcomp}} object.

-#' @param y numeric. Quantitative values used to color the points. 

-#' If rank is FALSE, all values must be positive integers and less than or equal to the length of y.

-#' @param rank logical. If TRUE (default) y will be transformed by the rank() function

+#' @param y numeric. Quantitative values used to color the points. If rank is 

+#'   FALSE, all values must be positive integers and less than or equal to the 

+#'   length of y.

+#' @param rank logical. If TRUE (default) y will be transformed by the rank() 

+#'   function

 #' @param ties_method character. ties.method used by the rank() function

-#' @param choices numeric. 2 principal components to plot. Default to first two PCs.

-#' @param expand numeric. value used to adjust the spread of the arrows relative

-#'   to the points.

+#' @param choices numeric. 2 principal components to plot. Default to first two

+#'   PCs.

+#' @param expand numeric. value used to adjust the spread of the arrows

+#'   relative to the points.

 #' @param ... arguments passed to plot.

-#'

+#'   

 #' @importFrom grDevices colorRampPalette

 #' @export

 #' 

 #' @return Invisibly returns scaled point coordinates used in plot.

-#'

+#'   

 #' @examples

 #' mat <- matrix(rnorm(1000), ncol=10)

 #' colnames(mat) <- paste("X", 1:ncol(mat), sep="")

-#'

+#' 

 #' pc <- prcomp(mat)

-#'

+#' 

 #' biplot_color(pc, rank(pc$x[,1]))

-#'

+#' 

 biplot_color <- function(x, y, rank = TRUE, 

-                         ties_method = c("max", "min", "first", "last", "random"),  

+                         ties_method = c("max", "min", 

+                                         "first", "last", "random"),

                          choices = 1:2, expand = 1, ...) {

   if(rank){

@@ -1,27 +1,22 @@

-## When porting the package to S4, we can make this a biplot method

-

-#' Another implementation of the biplot function

-#'

-#' Function to plot a biplot with no point labels and with points color-coded

-#' according to a certain quantitative variable, for instance the rank of the

-#' normalization performance or the expression of a certain gene.

+#' Function for biplotting with no point labels and with points color-coded according 

+#' to a quantitative variable. For example: the rank of normalization performance.

 #'

-#' This function implements the biplot only for \code{\link[stats]{prcomp}}

-#' objects. Eventually, we will turn this into an S4 method.

+#' This function implements biplot for \code{\link[stats]{prcomp}} objects.

 #'

-#' @param x the result of a call to \code{\link[stats]{prcomp}}.

-#' @param y an array of values used to color the points. 

+#' @param x \code{\link[stats]{prcomp}} object.

+#' @param y numeric. Quantitative values used to color the points. 

 #' If rank is FALSE, all values must be positive integers and less than or equal to the length of y.

 #' @param rank logical. If TRUE (default) y will be transformed by the rank() function

 #' @param ties_method character. ties.method used by the rank() function

-#' @param choices which principal components to plot. Only 2D plots are

-#'   possible for now. Default to first two PCs.

-#' @param expand numeric value used to adjust the spread of the arrows relative

+#' @param choices numeric. 2 principal components to plot. Default to first two PCs.

+#' @param expand numeric. value used to adjust the spread of the arrows relative

 #'   to the points.

-#' @param ... passed to plot.

+#' @param ... arguments passed to plot.

 #'

 #' @importFrom grDevices colorRampPalette

 #' @export

+#' 

+#' @return Invisibly returns scaled point coordinates used in plot.

 #'

 #' @examples

 #' mat <- matrix(rnorm(1000), ncol=10)

@@ -29,9 +24,11 @@

 #'

 #' pc <- prcomp(mat)

 #'

-#' biplot_colored(pc, rank(pc$x[,1]))

+#' biplot_color(pc, rank(pc$x[,1]))

 #'

-biplot_colored <- function(x, y, rank = TRUE, ties_method = c("max", "min", "first", "last", "random"),  choices=1:2, expand=1, ...) {

+biplot_color <- function(x, y, rank = TRUE, 

+                         ties_method = c("max", "min", "first", "last", "random"),  

+                         choices = 1:2, expand = 1, ...) {

   if(rank){

@@ -63,7 +60,9 @@ biplot_colored <- function(x, y, rank = TRUE, ties_method = c("max", "min", "fir

   ratio <- max(range(yy)/range(xx))/expand

-  cols <- rev(colorRampPalette(c("black","navyblue","mediumblue","dodgerblue3","aquamarine4","green4","yellowgreen","yellow"))(length(y)))[y]

+  cols <- rev(colorRampPalette(c("black","navyblue","mediumblue",

+                                 "dodgerblue3","aquamarine4","green4",

+                                 "yellowgreen","yellow"))(length(y)))[y]

   plot(xx, pch=19, col=cols, ...)

   labs <- rownames(yy)

@@ -10,7 +10,10 @@

 #' objects. Eventually, we will turn this into an S4 method.

 #'

 #' @param x the result of a call to \code{\link[stats]{prcomp}}.

-#' @param y the rank value that should be used to color the points.

+#' @param y an array of values used to color the points. 

+#' If rank is FALSE, all values must be positive integers and less than or equal to the length of y.

+#' @param rank logical. If TRUE (default) y will be transformed by the rank() function

+#' @param ties_method character. ties.method used by the rank() function

 #' @param choices which principal components to plot. Only 2D plots are

 #'   possible for now. Default to first two PCs.

 #' @param expand numeric value used to adjust the spread of the arrows relative

@@ -28,8 +31,29 @@

 #'

 #' biplot_colored(pc, rank(pc$x[,1]))

 #'

-biplot_colored <- function(x, y, choices=1:2, expand=1, ...) {

+biplot_colored <- function(x, y, rank = TRUE, ties_method = c("max", "min", "first", "last", "random"),  choices=1:2, expand=1, ...) {

+  if(rank){

+    

+    ties_method <- match.arg(ties_method)

+    y = rank(y,ties.method = ties_method)

+    

+  }else{

+    

+    if(any(abs(y - round(y)) > .Machine$double.eps^0.5)){

+      stop("ranks must be integer")

+    }else{y = as.integer(y)}

+    

+    if(any(y <= 0)){

+      stop("ranks must be positive")

+    }

+    

+    if(any(y > length(y))){

+      stop("ranks must be less than or equal to total number of elements")

+    }

+    

+  }

+  

   lam <- x$sdev[choices]

   n <- NROW(x$x)

   lam <- lam * sqrt(n)

@@ -46,4 +46,6 @@ biplot_colored <- function(x, y, choices=1:2, expand=1, ...) {

   text(yy/ratio, labels=labs, col=2)

   arrows(0, 0, yy[, 1] * 0.8/ratio, yy[, 2] * 0.8/ratio, col = 2, length = 0.1)

+

+  invisible(xx)

 }

new file mode 100644

@@ -0,0 +1,49 @@

+## When porting the package to S4, we can make this a biplot method

+

+#' Another implementation of the biplot function

+#'

+#' Function to plot a biplot with no point labels and with points color-coded

+#' according to a certain quantitative variable, for instance the rank of the

+#' normalization performance or the expression of a certain gene.

+#'

+#' This function implements the biplot only for \code{\link[stats]{prcomp}}

+#' objects. Eventually, we will turn this into an S4 method.

+#'

+#' @param x the result of a call to \code{\link[stats]{prcomp}}.

+#' @param y the rank value that should be used to color the points.

+#' @param choices which principal components to plot. Only 2D plots are

+#'   possible for now. Default to first two PCs.

+#' @param expand numeric value used to adjust the spread of the arrows relative

+#'   to the points.

+#' @param ... passed to plot.

+#'

+#' @importFrom grDevices colorRampPalette

+#' @export

+#'

+#' @examples

+#' mat <- matrix(rnorm(1000), ncol=10)

+#' colnames(mat) <- paste("X", 1:ncol(mat), sep="")

+#'

+#' pc <- prcomp(mat)

+#'

+#' biplot_colored(pc, rank(pc$x[,1]))

+#'

+biplot_colored <- function(x, y, choices=1:2, expand=1, ...) {

+

+  lam <- x$sdev[choices]

+  n <- NROW(x$x)

+  lam <- lam * sqrt(n)

+

+  xx <- t(t(x$x[, choices])/lam)

+  yy <- t(t(x$rotation[, choices]) * lam)

+

+  ratio <- max(range(yy)/range(xx))/expand

+

+  cols <- rev(colorRampPalette(c("black","navyblue","mediumblue","dodgerblue3","aquamarine4","green4","yellowgreen","yellow"))(length(y)))[y]

+  plot(xx, pch=19, col=cols, ...)

+

+  labs <- rownames(yy)

+

+  text(yy/ratio, labels=labs, col=2)

+  arrows(0, 0, yy[, 1] * 0.8/ratio, yy[, 2] * 0.8/ratio, col = 2, length = 0.1)

+}