Merge pull request #81 from vsimko/master

fixed issues #10 and #76

Author: vsimko

DESCRIPTION

@@ -1,15 +1,17 @@
 Package: corrplot
 Type: Package
 Title: Visualization of a Correlation Matrix
-Version: 0.81
-Date: 2017-02-07
+Version: 0.82
+Date: 2017-02-09
 Author: Taiyun Wei, Viliam Simko
 Suggests:
     knitr,
     testthat
 Maintainer: Taiyun Wei <weitaiyun@gmail.com>
 Description: A graphical display of a correlation matrix or general matrix.
-    It also contains some algorithms to do matrix reordering.
+    It also contains some algorithms to do matrix reordering. In addition,
+    corrplot is good at details, including choosing color, text labels,
+    color labels, layout, etc.
 License: GPL
 URL: https://github.com/taiyun/corrplot
 BugReports: https://github.com/taiyun/corrplot/issues

R/corrplot-package.R

@@ -0,0 +1,43 @@
+#' @docType package
+#' @name corrplot-package
+#'
+#' @title
+#' Visualization of a correlation matrix
+#'
+#' @description
+#' The corrplot package is a graphical display of a correlation matrix,
+#' confidence interval or general matrix. It also contains some algorithms to do
+#' matrix reordering. In addition, corrplot is good at details, including
+#' choosing color, text labels, color labels, layout, etc.
+#'
+#' @author Taiyun Wei (weitaiyun@@gmail.com)
+#' @author Viliam Simko (viliam.simko@@gmail.com)
+#'
+#' Maintainer: Taiyun Wei (weitaiyun@@gmail.com)
+#'
+#' @references
+#' Michael Friendly (2002).
+#' \emph{Corrgrams: Exploratory displays for correlation matrices}.
+#' The American Statistician, 56, 316--324.
+#'
+#' D.J. Murdoch, E.D. Chow (1996).
+#' \emph{A graphical display of large correlation matrices}.
+#' The American Statistician, 50, 178--180.
+#'
+#' @seealso
+#' The \code{plotcorr} function in the \code{ellipse} package and
+#' \code{corrgram} function in the \code{corrgram} package has some
+#' similarities.
+#'
+#' @keywords hplot
+#' @keywords correlation
+#' @keywords correlogram
+#' @keywords feature selection
+#' @keywords dimensionality reduction
+NULL
+
+.onAttach <- function(libname, pkgname) {
+  # just to show a startup message
+  message <- paste("corrplot", utils::packageVersion("corrplot"), "loaded")
+  packageStartupMessage(message, appendLF = TRUE)
+}

R/corrplot.R

@@ -229,7 +229,6 @@
 #'   ARSA, BBURCG, BBWRCG, MDS, TSP, Chen and so forth.
 #'
 #' @example vignettes/example-corrplot.R
-#' @keywords hplot
 #' @import graphics grDevices stats
 #' @export
 corrplot <- function(corr,
@@ -394,8 +393,8 @@ corrplot <- function(corr,
   apply_mat_filter <- function(mat) {
     x <- matrix(1:n * m, n, m)
     switch(type,
-        upper = mat[row(x) > col(x)] <- Inf,
-        lower = mat[row(x) < col(x)] <- Inf
+      upper = mat[row(x) > col(x)] <- Inf,
+      lower = mat[row(x) < col(x)] <- Inf
     )
 
     if (!diag) {
@@ -419,14 +418,14 @@ corrplot <- function(corr,
   # we use this for rending NA cells differently
   getPos.NAs <- function(mat) {
     tmp <- apply_mat_filter(mat)
-    ind  <- which(is.na(tmp), arr.ind = TRUE)
+    ind <- which(is.na(tmp), arr.ind = TRUE)
     Pos <- ind
     Pos[,1] <-  ind[,2]
     Pos[,2] <- -ind[,1] + 1 + n
     return(Pos)
   }
 
-  Pos  <- getPos.Dat(corr)[[1]]
+  Pos <- getPos.Dat(corr)[[1]]
 
   # rows
   n2 <- max(Pos[,2])
@@ -460,11 +459,11 @@ corrplot <- function(corr,
 
   ## assign colors
   assign.color <- function(dat = DAT, color = col){
-     newcorr <- (dat + 1) / 2
-     newcorr[newcorr <= 0]  <- 0
-     newcorr[newcorr >= 1]  <- 1 - 1e-16
+    newcorr <- (dat + 1) / 2
+    newcorr[newcorr <= 0]  <- 0
+    newcorr[newcorr >= 1]  <- 1 - 1e-16
 
-     color[floor(newcorr * length(color)) + 1] # new color returned
+    color[floor(newcorr * length(color)) + 1] # new color returned
   }
 
   col.fill <- assign.color()
@@ -503,39 +502,54 @@ corrplot <- function(corr,
   ## calculate label-text width approximately
   if (!add) {
     plot.new()
-    xlabwidth <- ylabwidth <- 0
 
+    # Issue #10: code from Sébastien Rochette (github user @statnmap)
+    xlabwidth <- max(strwidth(newrownames, cex = tl.cex))
+    ylabwidth <- max(strwidth(newcolnames, cex = tl.cex))
+    laboffset <- strwidth("W", cex = tl.cex) * tl.offset
+
+    # Issue #10
     for (i in 1:50) {
-      xlim <- c(m1 - 0.5 - xlabwidth,
-                m2 + 0.5 + mm * cl.ratio * (cl.pos == "r"))
-      ylim <- c(n1 - 0.5 - nn * cl.ratio * (cl.pos == "b"),
-                n2 + 0.5 + ylabwidth)
-      plot.window(xlim + c(-0.2, 0.2), ylim + c(-0.2, 0.2), asp = 1,
-                  xaxs = "i", yaxs = "i")
+      xlim <- c(
+        m1 - 0.5 - laboffset -
+          xlabwidth * (grepl("l", tl.pos) | grepl("d", tl.pos)),
+        m2 + 0.5 + mm * cl.ratio * (cl.pos == "r") +
+          xlabwidth * abs(cos(tl.srt * pi / 180)) * grepl("d", tl.pos)
+      ) + c(-0.35, 0.15) +
+          c(-1,0) * grepl("l", tl.pos) # margin between text and grid
+
+      ylim <- c(
+        n1 - 0.5 - nn * cl.ratio * (cl.pos == "b"),
+        n2 + 0.5 + laboffset +
+          ylabwidth * abs(sin(tl.srt * pi / 180)) * grepl("t", tl.pos)
+      ) +
+        c(-0.15, 0) +
+        c(0, -1) * (type == "upper") + # nasty hack
+        c(0,1) * grepl("d", tl.pos) # margin between text and grid
+
+      plot.window(xlim, ylim, asp = 1, xaxs = "i", yaxs = "i")
+
       x.tmp <- max(strwidth(newrownames, cex = tl.cex))
       y.tmp <- max(strwidth(newcolnames, cex = tl.cex))
 
-      if (min(x.tmp - xlabwidth, y.tmp - ylabwidth) < 0.0001) {
+      laboffset.tmp <- strwidth("W", cex = tl.cex) * tl.offset
+      if (max(x.tmp - xlabwidth,
+              y.tmp - ylabwidth,
+              laboffset.tmp - laboffset) < 1e-03) {
         break
       }
 
       xlabwidth <- x.tmp
       ylabwidth <- y.tmp
-    }
 
-    if (tl.pos == "n" || tl.pos == "d") {
-      xlabwidth <- ylabwidth <- 0
-    }
+      laboffset <- laboffset.tmp
 
-    if (tl.pos == "td") ylabwidth <- 0
-    if (tl.pos == "ld") xlabwidth <- 0
-
-    laboffset <- strwidth("W", cex = tl.cex) * tl.offset
-    xlim <- c(m1 - 0.5 - xlabwidth - laboffset,
-              m2 + 0.5 + mm * cl.ratio * (cl.pos == "r")) + c(-0.35, 0.15)
-    ylim <- c(n1 - 0.5 - nn * cl.ratio * (cl.pos == "b"),
-              n2 + 0.5 + ylabwidth * abs(sin(tl.srt * pi / 180)) + laboffset)
-            + c(-0.15, 0.35)
+      if (i == 50) {
+        warning(c("Not been able to calculate text margin, ",
+                  "please try again with a clean new empty window using ",
+                  "{plot.new(); dev.off()} or reduce tl.cex"))
+      }
+    }
 
     if (.Platform$OS.type == "windows") {
       grDevices::windows.options(width = 7,

R/corrplot.mixed.R

@@ -16,6 +16,8 @@
 #'   \code{\link{corrplot}}
 #' @param plotCI See the \code{plotCI} parameter in the function
 #'   \code{\link{corrplot}}
+#' @param lower.col Passed as \code{col} parameter to the lower matrix.
+#' @param upper.col Passed as \code{col} parameter to the upper matrix.
 #' @param \dots Additional arguments for corrplot's wrappers
 #'
 #' @author Taiyun Wei
@@ -29,6 +31,8 @@ corrplot.mixed <- function(
   diag = c("n", "l", "u"),
   bg = "white",
   addgrid.col = "grey",
+  lower.col = NULL,
+  upper.col = NULL,
   plotCI = c("n", "square", "circle", "rect"),
   ...)
 {
@@ -49,11 +53,13 @@ corrplot.mixed <- function(
   plotCI_upper <- adjust_plotCI(plotCI, upper)
 
   corrplot(corr, type = "upper", method = upper, diag = TRUE,
-           tl.pos = tl.pos, plotCI = plotCI_upper, ...)
+           tl.pos = tl.pos, plotCI = plotCI_upper,
+           col = upper.col, ...)
 
   corrplot(corr, add = TRUE, type = "lower", method = lower,
            diag = (diag == "l"),
-           tl.pos = "n", cl.pos = "n", plotCI = plotCI_lower, ...)
+           tl.pos = "n", cl.pos = "n", plotCI = plotCI_lower,
+           col = lower.col, ...)
 
   if (diag == "n" && tl.pos != "d") {
       symbols(1:n, n:1, add = TRUE, bg = bg, fg = addgrid.col,

inst/CITATION

@@ -2,12 +2,12 @@ bibentry("Manual",
 	title="R package 'corrplot': Visualization of a correlation matrix",
 	author="Taiyun Wei and Viliam Simko",
 	year="2017",
-	note="(Version 0.81)",
+	note="(Version 0.82)",
 	url="https://github.com/taiyun/corrplot",
 
 	textVersion =
   	paste("T. Wei and V. Simko (2016). ",
-  			"R package 'corrplot': Visualization of a correlation matrix (Version 0.81). ",
+  			"R package 'corrplot': Visualization of a correlation matrix (Version 0.82). ",
   			"Available from https://github.com/taiyun/corrplot",
   			sep=""),
 

inst/NEWS

@@ -1,13 +1,22 @@
+		CHANGES IN corrplot VERSION 0.81
+
+CHANGES
+  * Fixed #79: added parameter `win.asp` to control aspect ratio
+  * Fixed #18: parameter `outline` combined with `method="pie"` controls
+    the color of the otline circle of each pie.
+  * updated vignette
+
+
 		CHANGES IN corrplot VERSION 0.80
 
 CHANGES
-  * Fixed #70, Enable to plot a matrix with NA when 'is.corr = F'
+  * Fixed #70: Enable to plot a matrix with NA when 'is.corr = F'
 
 
 		CHANGES IN corrplot VERSION 0.77
 
 CHANGES
-  * Fixed #58, make sure the margin is correct in corrplot.mixed().
+  * Fixed #58: make sure the margin is correct in corrplot.mixed().
   * Revised document.
 
 

man/corrplot-package.Rd

@@ -86,15 +86,15 @@ test_that("Issue #21: plotCI=rect incompatible with some methods", {
   L <- M - 0.1
   U <- M + 0.1
   expect_equal(corrplot.mixed(M, lower = "circle", upper = "number",
-                              low = L, upp = U, plotCI = "rect"), M)
+                              lowCI = L, uppCI = U, plotCI = "rect"), M)
   expect_equal(corrplot.mixed(M, lower = "number", upper = "circle",
-                              low = L, upp = U, plotCI = "rect"), M)
+                              lowCI = L, uppCI = U, plotCI = "rect"), M)
   expect_equal(corrplot.mixed(M, lower = "circle", upper = "square",
-                              low = L, upp = U, plotCI = "rect"), M)
+                              lowCI = L, uppCI = U, plotCI = "rect"), M)
   expect_equal(corrplot.mixed(M, lower = "ellipse", upper = "square",
-                              low = L, upp = U, plotCI = "rect"), M)
+                              lowCI = L, uppCI = U, plotCI = "rect"), M)
   expect_equal(corrplot.mixed(M, lower = "pie", upper = "square",
-                              low = L, upp = U, plotCI = "rect"), M)
+                              lowCI = L, uppCI = U, plotCI = "rect"), M)
 })
 
 test_that("Issue #43: Return value should be the same as corrplot function", {
@@ -208,3 +208,10 @@ test_that("Issue #18", {
   expect_silent(corrplot(M, method = "pie", outline = TRUE))
   expect_silent(corrplot(M, method = "pie", outline = "white"))
 })
+
+test_that("Issue #76: separate `col` parameters corrplot.mixed", {
+  M <- cor(mtcars)
+  expect_silent(corrplot.mixed(M, lower.col = "black"))
+  expect_silent(corrplot.mixed(M, lower = "circle",
+                               upper = "number", upper.col = "black"))
+})