1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
|
#############################################################
# #
# heatmap.circular function #
# Author: Claudio Agostinelli #
# E-mail: claudio.agostinelli@unitn.it #
# Date: December, 27, 2015 #
# Version: 0.8 #
# #
# Copyright (C) 2015 Claudio Agostinelli #
# #
#############################################################
## This is a modified version of the heatmap function in package stats.
## The original heatmap function is made by Andy Liaw; modified RG, MM :
#############################################################
heatmap.circular <- function (x, Rowv=NULL, Colv=if(symm)"Rowv" else NULL,
distfun = dist.circular, hclustfun = hclust,
reorderfun = function(d,w) reorder(d,w),
add.expr, symm = FALSE, revC = identical(Colv, "Rowv"),
na.rm=TRUE,
margins = c(5, 5), lwid=c(1,4), lhei=c(1,4),
ColSideColors, RowSideColors, NAColors="black",
cexRow = 0.2 + 1/log10(nr), cexCol = 0.2 + 1/log10(nc),
labRow = NULL, labCol = NULL, main = NULL, xlab = NULL, ylab = NULL,
keep.dendro = FALSE,
annotate.expr, annotate=rep(NA, 4),
verbose = getOption("verbose"), ...) {
if(length(di <- dim(x)) != 2 || !is.numeric(x))
stop("'x' must be a numeric matrix")
nr <- di[1]
nc <- di[2]
if(nr <= 1 || nc <= 1)
stop("'x' must have at least 2 rows and 2 columns")
if(!is.numeric(margins) || length(margins) != 2)
stop("'margins' must be a numeric vector of length 2")
doRdend <- !identical(Rowv,NA)
doCdend <- !identical(Colv,NA)
## by default order by row/col means
if(is.null(Rowv)) Rowv <- rowMeans(x, na.rm = na.rm)
if(is.null(Colv)) Colv <- colMeans(x, na.rm = na.rm)
## get the dendrograms and reordering indices
if(doRdend) {
if(inherits(Rowv, "dendrogram"))
ddr <- Rowv
else {
hcr <- hclustfun(distfun(x))
ddr <- as.dendrogram(hcr)
if(!is.logical(Rowv) || Rowv)
ddr <- reorderfun(ddr, Rowv)
}
if(nr != length(rowInd <- order.dendrogram(ddr)))
stop("row dendrogram ordering gave index of wrong length")
}
else rowInd <- 1L:nr
if(doCdend) {
if(inherits(Colv, "dendrogram"))
ddc <- Colv
else if(identical(Colv, "Rowv")) {
if(nr != nc)
stop('Colv = "Rowv" but nrow(x) != ncol(x)')
ddc <- ddr
}
else {
hcc <- hclustfun(distfun(if(symm)x else t(x)))
ddc <- as.dendrogram(hcc)
if(!is.logical(Colv) || Colv)
ddc <- reorderfun(ddc, Colv)
}
if(nc != length(colInd <- order.dendrogram(ddc)))
stop("column dendrogram ordering gave index of wrong length")
}
else colInd <- 1L:nc
## reorder x
x <- x[rowInd, colInd]
labRow <-
if(is.null(labRow))
if(is.null(rownames(x))) (1L:nr)[rowInd] else rownames(x)
else labRow[rowInd]
labCol <-
if(is.null(labCol))
if(is.null(colnames(x))) (1L:nc)[colInd] else colnames(x)
else labCol[colInd]
## Calculate the plot layout
lmat <- rbind(c(NA, 3), 2:1)
lwid <- c(if(doRdend) lwid[1] else 0.05, lwid[2])
lhei <- c((if(doCdend) lhei[1] else 0.05) + if(!is.null(main)) 0.2 else 0, lhei[2])
if(!missing(ColSideColors)) { ## add middle row to layout
if(!is.character(ColSideColors) || length(ColSideColors) != nc)
stop("'ColSideColors' must be a character vector of length ncol(x)")
lmat <- rbind(lmat[1,]+1, c(NA,1), lmat[2,]+1)
lhei <- c(lhei[1], 0.2, lhei[2])
}
if(!missing(RowSideColors)) { ## add middle column to layout
if(!is.character(RowSideColors) || length(RowSideColors) != nr)
stop("'RowSideColors' must be a character vector of length nrow(x)")
lmat <- cbind(lmat[,1]+1, c(rep(NA, nrow(lmat)-1), 1), lmat[,2]+1)
lwid <- c(lwid[1], 0.2, lwid[2])
}
# Annotate setup
if (!is.na(annotate[1])) {
lmat <- rbind(lmat, c(rep(NA, ncol(lmat)-1), max(lmat, na.rm=TRUE)+1))
lhei <- c(lhei, annotate[1])
}
if (!is.na(annotate[3])) {
lmat <- rbind(c(rep(NA, ncol(lmat)-1), max(lmat, na.rm=TRUE)+1), lmat)
lhei <- c(annotate[3], lhei)
}
if (!is.na(annotate[2])) {
lmat <- cbind(c(rep(NA, nrow(lmat)-1-!is.na(annotate[1])), max(lmat, na.rm=TRUE)+1, rep(NA, !is.na(annotate[1]))), lmat)
lwid <- c(annotate[2], lwid)
}
for (i in 4:length(annotate)) {
if (!is.na(annotate[i])) {
lmat <- cbind(lmat, c(rep(NA, nrow(lmat)-1-!is.na(annotate[1])), max(lmat, na.rm=TRUE)+1, rep(NA, !is.na(annotate[1]))))
lwid <- c(lwid, annotate[i])
}
}
lmat[is.na(lmat)] <- 0
if(verbose) {
cat("layout: widths = ", lwid, ", heights = ", lhei,"; lmat=\n")
print(lmat)
}
## Graphics `output' -----------------------
op <- par(no.readonly = TRUE)
on.exit(par(op))
layout(lmat, widths = lwid, heights = lhei, respect = TRUE)
## draw the side bars
if(!missing(RowSideColors)) {
par(mar = c(margins[1],0, 0,0.5))
image(rbind(1L:nr), col = RowSideColors[rowInd], axes = FALSE)
}
if(!missing(ColSideColors)) {
par(mar = c(0.5,0, 0,margins[2]))
image(cbind(1L:nc), col = ColSideColors[colInd], axes = FALSE)
}
## draw the main carpet
par(mar = c(margins[1], 0, 0, margins[2]))
if(!symm)
x <- t(x)
if(revC) { # x columns reversed
iy <- nr:1
ddr <- rev(ddr)
x <- x[,iy]
} else iy <- 1L:nr
image(1L:nc, 1L:nr, x, xlim = 0.5+ c(0, nc), ylim = 0.5+ c(0, nr),
axes = FALSE, xlab = "", ylab = "", zlim=c(0,2*pi), ...)
xna <- is.na(x)
mode(xna) <- "numeric"
xna[xna==0] <- NA
image(1L:nc, 1L:nr, xna, col=NAColors, add=TRUE)
axis(1, 1L:nc, labels= labCol, las= 2, line= -0.5, tick= 0, cex.axis= cexCol)
if(!is.null(xlab)) mtext(xlab, side = 1, line = margins[1] - 1.25)
axis(4, iy, labels= labRow, las= 2, line= -0.5, tick= 0, cex.axis= cexRow)
if(!is.null(ylab)) mtext(ylab, side = 4, line = margins[2] - 1.25)
if (!missing(add.expr))
eval.parent(substitute(add.expr))
## the two dendrograms :
par(mar = c(margins[1], 0, 0, 0))
if(doRdend)
plot(ddr, horiz = TRUE, axes = FALSE, yaxs = "i", leaflab = "none")
else frame()
par(mar = c(0, 0, if(!is.null(main)) 1 else 0, margins[2]))
if(doCdend)
plot(ddc, axes = FALSE, xaxs = "i", leaflab = "none")
else if(!is.null(main)) frame()
## title
if(!is.null(main)) title(main, cex.main = 1.5*op[["cex.main"]])
par(mar = c(0, 0, 0, margins[2]))
if (!is.na(annotate[1]))
eval(annotate.expr[[1]])
if (!is.na(annotate[3]))
eval(annotate.expr[[3]])
par(mar = c(margins[1], 0, 0, 0))
if (!is.na(annotate[2]))
eval(annotate.expr[[2]])
for (i in 4:length(annotate)) {
if (!is.na(annotate[i]))
eval(annotate.expr[[i]])
}
invisible(list(rowInd = rowInd, colInd = colInd,
Rowv = if(keep.dendro && doRdend) ddr,
Colv = if(keep.dendro && doCdend) ddc ))
}
|
