Commit ⋅ taiyun/corrplot

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R/corrplot.R changed.

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vignettes/corrplot-intro.Rmd has changed.

man/corrplot.Rd has changed.

@@ -42,6 +42,10 @@

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#'   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 @@

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#'   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 @@

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#'
#' @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 @@

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#' @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 @@

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                    '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 @@

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  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 @@

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    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 @@

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      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')
      #}

    }


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    patch: false

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266	267		#' @export
267	268		corrplot = function(corr,
268	269		method = c('circle', 'square', 'ellipse', 'number', 'shade', 'color', 'pie'),
269		-	type = c('full', 'lower', 'upper'), col = NULL, col.lim = NULL, bg = 'white',
270		-	title = '', add = FALSE, diag = TRUE, outline = FALSE,
	270	+	type = c('full', 'lower', 'upper'), col = NULL, col.lim = NULL, is.corr = TRUE,
	271	+	bg = 'white', title = '', add = FALSE, diag = TRUE, outline = FALSE,
271	272		mar = c(0, 0, 0, 0),
272	273
273	274		addgrid.col = NULL, addCoef.col = NULL, addCoefasPercent = FALSE,

277	278		'average', 'mcquitty', 'median', 'centroid'),
278	279		addrect = NULL, rect.col = 'black', rect.lwd = 2,
279	280
280		-	is.corr = TRUE, ignoreSign = FALSE,
281		-
282	281		tl.pos = NULL, tl.cex = 1,
283	282		tl.col = 'red', tl.offset = 0.4, tl.srt = 90,
284	283

290	289		addshade = c('negative', 'positive', 'all'),
291	290		shade.lwd = 1, shade.col = 'white',
292	291
	292	+	transKeepSign = TRUE,
	293	+
293	294		p.mat = NULL, sig.level = 0.05,
294	295		insig = c('pch', 'p-value', 'blank', 'n', 'label_sig'),
295	296		pch = 4, pch.col = 'black', pch.cex = 3,

327	328		addgrid.col = switch(method, color = NA, shade = NA, 'grey')
328	329		}
329	330
	331	+	if(!is.corr & !transKeepSign & method %in% c('circle', 'square', 'ellipse', 'shade', 'pie')) {
	332	+	stop("method should not be in c('circle', 'square', 'ellipse', 'shade', 'pie') when transKeepSign = FALSE")
	333	+	}
	334	+
330	335		# Issue #142
331	336		# checks for all values that are not missing
332	337		if (any(corr[!is.na(corr)] < col.lim[1]) \|\| any(corr[!is.na(corr)] > col.lim[2])) {

389	394		warning('col.lim interval too wide, please set a suitable value')
390	395		}
391	396
392		-	# all negative or positive or NOT keepSign, trans to [0, 1]
393		-	if (c_max <= 0 \| c_min>=0 \| ignoreSign) {
	397	+	# all negative or positive or NOT transkeepSign, trans to [0, 1]
	398	+	if (c_max <= 0 \| c_min>=0 \| !transKeepSign) {
394	399		intercept = - col.lim[1]
395	400		zoom = 1 / (diff(col.lim))
396	401
397		-
398		-	if(col.lim[1] * col.lim[2] < 0) {
399		-	warning('col.lim interval not suitable to the matrix')
400		-	}
	402	+	#if(col.lim[1] * col.lim[2] < 0) {
	403	+	# warning('col.lim interval not suitable to the matrix')
	404	+	#}
401	405
402	406		}
403	407

42	42		#' are still distributed uniformly in [-1, 1], it only affect the display
43	43		#' on color-legend.
44	44		#'
	45	+	#' @param is.corr Logical, whether the input matrix is a correlation matrix or
	46	+	#' not. We can visualize the non-correlation matrix by setting
	47	+	#' \code{is.corr = FALSE}.
	48	+	#'
45	49		#'
46	50		#' @param bg The background color.
47	51		#'

99	103		#' valid when \code{addrect} is equal or greater than 1.
100	104		#'
101	105		#'
102		-	#' @param is.corr Logical, whether the input matrix is a correlation matrix or
103		-	#' not. We can visualize the non-correlation matrix by setting
104		-	#' \code{is.corr = FALSE}.
105		-	#'
106		-	#' @param ignoreSign Logical, whether or not to ignore matrix values' sign when assigning colors
107		-	#’ for non-corr matrix.
108		-	#' Only valid when \code{is.corr = FALSE}. The default value is \code{FALSE}.
109		-	#'
110		-	#'
111	106		#' @param tl.pos Character or logical, position of text labels. If character, it
112	107		#' must be one of \code{'lt'}, \code{'ld'}, \code{'td'}, \code{'d'} or
113	108		#' \code{'n'}. \code{'lt'}(default if \code{type=='full'}) means left and top,

169	164		#'
170	165		#' @param shade.col The color of shade line.
171	166		#'
	167	+	#' @param transKeepSign Logical, whether or not to keep matrix values' sign when
	168	+	#' transforming non-corr matrix for plotting.
	169	+	#' Only valid when \code{is.corr = FALSE}. The default value is \code{TRUE}.
	170	+	#'
	171	+	#' NOTE: If \code{FALSE},the non-corr matrix will be
	172	+	#'
172	173		#' @param p.mat Matrix of p-value, if \code{NULL}, parameter \code{sig.level},
173	174		#' \code{insig}, \code{pch}, \code{pch.col}, \code{pch.cex} are invalid.
174	175		#'

1	comment: false
2
3	coverage:
4	status:
5	project: false
6	patch: false

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