From d4cd81caffba1c01a131374aa9cc06921f9445d1 Mon Sep 17 00:00:00 2001
From: jbedia <joaquin.bedia@gmail.com>
Date: Fri, 22 Aug 2014 13:42:14 +0200
Subject: [PATCH] plotEOF improvements

---
 R/plotEOF.R | 52 +++++++++++++++++++++++++++++++++-------------------
 1 file changed, 33 insertions(+), 19 deletions(-)

diff --git a/R/plotEOF.R b/R/plotEOF.R
index 1be3190e..79be71d8 100644
--- a/R/plotEOF.R
+++ b/R/plotEOF.R
@@ -1,26 +1,27 @@
 #' @title Plot an arbitrary number of EOFs
 #' 
 #' @description Plots an arbitrary number of EOFs. Useful to have a quick overview of the main spatial modes
-#'  of a field.
+#'  of a (possibly multimember) field.
+#'  
 #' @param prinCompObj A PCA object as returned by \code{\link{prinComp}}
 #' @param var Character string indicating the variable whose EOFs are to be displayed. If the PCA analysis has
 #' been applied to 1 single field, this argument can be omitted.
 #' @param n.eofs Number of EOFs to be displayed. Default to NULL, indicating that all computed EOFS
 #' will be represented
+#' @param member An integer indicating the position of the member whose EOFs are to be displayed. Default 1, 
+#' corresponding to the first member. Ignored for non multimember fields.
 #' 
 #' @return A plot with as many panels as EOFs requested, in the original units of the variable
-#' @export
+#' # @export
 #' @author J. Bedia \email{joaquin.bedia@@gmail.com}
 #' 
-#' @family multifield
-#' @family loading.grid
+#' @seealso \code{\link{prinComp}}
 #' 
 #' @examples \dontrun{ 
 #' # Winter temperature at 850 mb isobaric surface pressure level is loaded (period 1981--2010):
-#' ncep <- file.path(find.package("downscaleR"), "datasets/reanalysis/Iberia_NCEP/Iberia_NCEP.ncml")
-#' field <- loadGridData(ncep, var = "ta@@85000", season = c(12,1,2), years = 1981:2010)
+#' data(iberia_ncep_ta850)
 #' # PCA analysis, retaining the PCs that explain 95\% of the total variance:
-#' pca <- prinComp(field, v.exp = .95)
+#' pca <- prinComp(iberia_ncep_ta850, v.exp = .95)
 #' # Plot of all EOFs
 #' plotEOF(pca)
 #' # Plot the first 4 EOFs:
@@ -28,6 +29,7 @@
 #' 
 #' # Example with PCA analysis of a multifield (multiple variables)
 #' load geopotential heigth at 500 mb, temperature at 1000 mb and sea-level pressure
+#' ncep <- file.path(find.package("downscaleR"), "datasets/reanalysis/Iberia_NCEP/Iberia_NCEP.ncml")
 #' multifield <- loadMultiField(ncep, vars = c("z@@50000", "ta@@100000", "psl"), season = c(12,1,2), years = 1981:2010)
 #' # PCA analysis, retaining the first 9 PCs of each variable:
 #' pca2 <- prinComp(multifield, n.eofs = 9)
@@ -37,9 +39,11 @@
 #' plotEOF(pca2, "ta", n.eofs = 4)
 #' plotEOF(pca2, "psl", n.eofs = 2)
 #' }
+#' 
 
 
-plotEOF <- function(prinCompObj, var = NULL, n.eofs = NULL) {
+plotEOF <- function(prinCompObj, var = NULL, member = 1, n.eofs = NULL) {
+      member <- as.integer(member)
       varNames <- attributes(prinCompObj)$names
       if (length(varNames) == 1) {
             ind.var <- 1
@@ -55,18 +59,28 @@ plotEOF <- function(prinCompObj, var = NULL, n.eofs = NULL) {
                   stop("It is not possible to display the combined EOF")
             }
       }
-      pco <- prinCompObj[[ind.var]]
-      x <- attributes(prinCompObj)$xCoords
-      y <- attributes(prinCompObj)$yCoords
+      if (length(prinCompObj[[1]]) == 1) {
+            if (member != 1) {
+                  warning("Argument 'member' was ignored")
+            }
+            member <- 1
+      }
+      if (!(member %in% 1:length(prinCompObj[[1]]))) {
+            stop("'member' value must be between 1 and the total number of members (", length(prinCompObj[[1]]), " in this case)")
+      }
+      eofs <- prinCompObj[[ind.var]][[member]]$EOFs
       if (is.null(n.eofs)) {
-            n.eofs <- ncol(pco$EOFs)
-      } else if (n.eofs > ncol(pco$EOFs)) {
-            warning("The requested number of EOFs (",n.eofs,") is larger than actual number of EOFs available (",ncol(pco$EOFs),")\nOnly the available EOFs were displayed")
-            n.eofs <- ncol(pco$EOFs)
+            n.eofs <- ncol(eofs)
+      }
+      if (!(n.eofs %in% 1:ncol(eofs))) {
+            stop("'n.eofs' value must be between 1 and the total number of possible EOFs (", ncol(eofs), " in this case)")
       }
-      mu <- attributes(pco)$"scaled:center"
-      sigma <- attributes(pco)$"scaled:scale"
-      out <- list("Data" = mat2Dto3Darray(t(pco$EOFs[ ,1:n.eofs] * sigma + mu), x, y), "xyCoords" = list(x = x, y = y))
-      multiPlot(out, split.dim.name = "time", title = paste("EOF",1:n.eofs))
+      x <- attributes(prinCompObj)$xCoords
+      y <- attributes(prinCompObj)$yCoords
+      mu <- attributes(prinCompObj[[ind.var]][[member]])$"scaled:center"
+      sigma <- attributes(prinCompObj[[ind.var]][[member]])$"scaled:scale"
+      out <- list("Data" = mat2Dto3Darray(t(eofs[ ,1:n.eofs] * sigma + mu), x, y), "xyCoords" = list(x = x, y = y))
+      multiPlot(out, split.dim.name = "time", titles = paste("EOF", 1:n.eofs))
 }
 # End
+