Merge pull request #258 from taiyun/dev

rename parameter

DESCRIPTION

@@ -2,7 +2,7 @@ Package: corrplot
 Type: Package
 Title: Visualization of a Correlation Matrix
 Version: 0.93
-Date: 2022-08-29
+Date: 2022-08-31
 Authors@R: c(
   person('Taiyun', 'Wei', email = 'weitaiyun@gmail.com', role = c('cre', 'aut')),
   person('Viliam', 'Simko', email = 'viliam.simko@gmail.com', role = 'aut'),

NEWS.md

@@ -4,8 +4,7 @@
 
   *  Fix #247: `addgrid.col` and `bg` don't work in mixed plot. (thanks, @ZoomMan91)
   *  Fix #246: using `insig = "n"` and `p.mat` sometimes causes an error. (thanks, @Sumidu)
-  *  Fix #255: add new parameter `ignoreSign`, whether or not to ignore matrix values' sign when assigning colors for non-corr matrix.
-
+  *  Fix #255: add new parameter `transKeepSign`, whether or not to keep matrix values' sign when transforming non-corr matrix.
 
 # corrplot 0.92
 

R/corrplot.R

@@ -42,6 +42,10 @@
 #'   are still distributed uniformly in [-1, 1], it only affect the display
 #'   on color-legend.
 #'
+#' @param is.corr Logical, whether the input matrix is a correlation matrix or
+#'   not. We can visualize the non-correlation matrix by setting
+#'   \code{is.corr = FALSE}.
+#'
 #'
 #' @param bg The background color.
 #'
@@ -99,15 +103,6 @@
 #'   valid when \code{addrect} is equal or greater than 1.
 #'
 #'
-#' @param is.corr Logical, whether the input matrix is a correlation matrix or
-#'   not. We can visualize the non-correlation matrix by setting
-#'   \code{is.corr = FALSE}.
-#'
-#' @param ignoreSign Logical, whether or not to ignore matrix values' sign when assigning colors
-#’   for non-corr matrix.
-#'   Only valid when \code{is.corr = FALSE}. The default value is \code{FALSE}.
-#'
-#'
 #' @param tl.pos Character or logical, position of text labels. If character, it
 #'   must be one of \code{'lt'}, \code{'ld'}, \code{'td'}, \code{'d'} or
 #'   \code{'n'}. \code{'lt'}(default if \code{type=='full'}) means left and top,
@@ -169,6 +164,12 @@
 #'
 #' @param shade.col The color of shade line.
 #'
+#' @param transKeepSign Logical, whether or not to keep matrix values' sign when
+#'   transforming non-corr matrix for plotting.
+#'   Only valid when \code{is.corr = FALSE}. The default value is \code{TRUE}.
+#'
+#'   NOTE: If \code{FALSE},the non-corr matrix will be
+#'
 #' @param p.mat Matrix of p-value, if \code{NULL}, parameter \code{sig.level},
 #'   \code{insig}, \code{pch}, \code{pch.col}, \code{pch.cex} are invalid.
 #'
@@ -266,8 +267,8 @@
 #' @export
 corrplot = function(corr,
   method = c('circle', 'square', 'ellipse', 'number', 'shade', 'color', 'pie'),
-  type = c('full', 'lower', 'upper'), col = NULL, col.lim = NULL, bg = 'white',
-  title = '', add = FALSE,   diag = TRUE, outline = FALSE,
+  type = c('full', 'lower', 'upper'), col = NULL, col.lim = NULL, is.corr = TRUE,
+  bg = 'white',   title = '', add = FALSE, diag = TRUE, outline = FALSE,
   mar = c(0, 0, 0, 0),
 
   addgrid.col = NULL, addCoef.col = NULL, addCoefasPercent = FALSE,
@@ -277,8 +278,6 @@ corrplot = function(corr,
                     'average', 'mcquitty', 'median', 'centroid'),
   addrect = NULL, rect.col = 'black', rect.lwd = 2,
 
-  is.corr = TRUE, ignoreSign = FALSE,
-
   tl.pos = NULL, tl.cex = 1,
   tl.col = 'red', tl.offset = 0.4, tl.srt = 90,
 
@@ -290,6 +289,8 @@ corrplot = function(corr,
   addshade = c('negative', 'positive', 'all'),
   shade.lwd = 1, shade.col = 'white',
 
+  transKeepSign = TRUE,
+
   p.mat = NULL, sig.level = 0.05,
   insig = c('pch', 'p-value', 'blank', 'n', 'label_sig'),
   pch = 4, pch.col = 'black', pch.cex = 3,
@@ -327,6 +328,10 @@ corrplot = function(corr,
     addgrid.col = switch(method, color = NA, shade = NA, 'grey')
   }
 
+  if(!is.corr & !transKeepSign & method %in% c('circle', 'square', 'ellipse', 'shade', 'pie')) {
+    stop("method should not be in c('circle', 'square', 'ellipse', 'shade', 'pie') when transKeepSign = FALSE")
+  }
+
   # Issue #142
   # checks for all values that are not missing
   if (any(corr[!is.na(corr)] < col.lim[1]) || any(corr[!is.na(corr)] > col.lim[2])) {
@@ -389,15 +394,14 @@ corrplot = function(corr,
       warning('col.lim interval too wide, please set a suitable value')
     }
 
-    # all negative or positive or NOT keepSign, trans to [0, 1]
-    if (c_max <= 0 | c_min>=0 | ignoreSign) {
+    # all negative or positive or NOT transkeepSign, trans to [0, 1]
+    if (c_max <= 0 | c_min>=0 | !transKeepSign) {
       intercept = - col.lim[1]
       zoom = 1 / (diff(col.lim))
 
-
-      if(col.lim[1] * col.lim[2] < 0) {
-        warning('col.lim interval not suitable to the matrix')
-      }
+      #if(col.lim[1] * col.lim[2] < 0) {
+      #  warning('col.lim interval not suitable to the matrix')
+      #}
 
     }
 

vignettes/corrplot-intro.Rmd

@@ -378,11 +378,15 @@ corrplot(N1, is.corr = FALSE, col.lim = c(20, 30), method = 'color', tl.pos = 'n
 ## matrix in [-15, 10]
 N2 = matrix(runif(80, -15, 10), 8)
 
-## using sequential colors and ignore matrix values' sign when assigning colors
-corrplot(N2, is.corr = FALSE, ignoreSign = TRUE, method = 'color', col.lim = c(-15, 10), 
-         tl.pos = 'n', col = COL1("YlOrBr"), cl.pos = 'b', addCoef.col = 'grey50')
+## using sequential colors, transKeepSign = FALSE
+corrplot(N2, is.corr = FALSE, transKeepSign = FALSE, method = 'color', col.lim = c(-15, 10), 
+         tl.pos = 'n', col = COL1('YlGn'), cl.pos = 'b', addCoef.col = 'grey50')
 
-## using diverging colors and don't ignore matrix values' sign when assigning colors
+## using diverging colors, transKeepSign = TRUE (default)
+corrplot(N2, is.corr = FALSE, col.lim = c(-15, 10), 
+         tl.pos = 'n', col = COL2('PiYG'), cl.pos = 'b', addCoef.col = 'grey50')
+
+## using diverging colors
 corrplot(N2, is.corr = FALSE, method = 'color', col.lim = c(-15, 10), tl.pos = 'n',
          col = COL2('PiYG'), cl.pos = 'b', addCoef.col = 'grey50')
 ```