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
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
|
xgobi <- function(matrx,
collab = dimnames(matrx)[[2]],
rowlab = dimnames(matrx)[[1]],
colors = NULL,
glyphs = NULL,
erase = NULL,
lines = NULL,
linecolors = NULL,
resources = NULL,
title = NULL,
vgroups = NULL,
std = "mmx",
dev = 2.0,
nlinkable = NULL,
subset = NULL,
display = NULL)
{
if (!missing(matrx))
{
### data matrix ###
x <- eval(matrx)
if (sum(abs(x[!is.na(x)])) == Inf > 0)
{
cat("Sorry, xgobi can't handle Infs\n")
return()
}
dfile <- tempfile("unix")
cat(t(x), file = dfile, fill = 80)
### Missing values, if present ###
#if (sum(is.na(x)) > 0) {
# x.missing <- is.na(x)
# x.missing[x.missing == FALSE] <- 0
# x.missing[x.missing == TRUE] <- 1
# missingfile <- paste(dfile, ".missing", sep="")
# cat(t(x.missing), file = missingfile, fill = 80)
#}
### Use the C code to do this ###
### Column labels ###
if (missing(collab))
collab <- dimnames(x)[[2]]
else {
# check data type
if (!is.vector(collab) || !is.character(collab)) {
cat("The 'collab' argument needs to be a character vector\n")
return()
}
}
if (length(collab) > 0)
{
colfile <- paste(dfile, ".col", sep="")
cat(collab, file = colfile, sep="\n")
}
### Row labels ###
if (missing(rowlab))
rowlab <- dimnames(x)[[1]]
else {
# check data type
if (!is.vector(rowlab) || !is.character(rowlab)) {
cat("The 'rowlab' argument needs to be a character vector\n")
return()
}
}
if (length(rowlab) > 0) {
rowfile <- paste(dfile, ".row", sep="")
cat(rowlab, file = rowfile, sep="\n")
}
### Variable groups ###
if (!missing(vgroups)) {
# check data type
if (!is.vector(vgroups) || !is.numeric(vgroups)) {
cat("The 'vgroups' argument needs to be a numeric vector\n")
return()
}
vgroupfile <- paste(dfile, ".vgroups", sep="")
cat(vgroups, file = vgroupfile, sep="\n")
}
### Colors ###
if (!missing(colors)) {
# check data type
if (!is.vector(colors) || !is.character(colors)) {
cat("The 'colors' argument needs to be a character vector\n")
return()
}
colorfile <- paste(dfile, ".colors", sep="")
cat(colors, file = colorfile, sep="\n")
}
### Glyphs ###
if (!missing(glyphs))
{
# check data type
if (!is.vector(glyphs) || !is.numeric(glyphs)) {
cat("The 'glyphs' argument needs to be a numeric vector\n")
return()
}
glyphfile <- paste(dfile, ".glyphs", sep="")
cat(glyphs, file = glyphfile, sep="\n")
}
### Erase ###
if (!missing(erase))
{
# check data type
if (!is.vector(erase) || !is.numeric(erase)) {
cat("The 'erase' argument needs to be a numeric vector\n")
return()
}
erasefile <- paste(dfile, ".erase", sep="")
cat(erase, file = erasefile, sep="\n")
}
### Connected lines ###
if (!missing(lines))
{
# check data type
if (!is.matrix(lines) || !is.numeric(lines) || dim(lines)[2] != 2) {
cat("The 'lines' argument must be a numeric 2-column matrix\n")
return()
}
linesfile <- paste(dfile, ".lines", sep="")
unix(paste("rm -f", linesfile), output=F)
if (nrow(lines) > 0) {
for (i in 1:nrow(lines))
cat(lines[i,], "\n", file = linesfile, append=T)
}
### Line colors ###
if (!missing(linecolors)) {
# check data type
if (!is.vector(linecolors) || !is.character(linecolors)) {
cat("The 'linecolors' argument must be a character vector\n")
return()
}
linecolorfile <- paste(dfile, ".linecolors", sep="")
cat(linecolors, file = linecolorfile, sep="\n")
}
}
### Resources ###
if (!missing(resources))
{
# check data type
if (!is.vector(resources) || !is.character(resources)) {
cat("The 'resources' argument must be a character vector\n")
return()
}
resourcefile <- paste(dfile, ".resources", sep="")
cat(resources, file = resourcefile, sep ="\n")
}
### nlinkable ###
if (!missing(nlinkable)) {
# check data type
nlinkable <- as.integer(nlinkable)
if (length(nlinkable) > 1) {
cat("The 'nlinkable' argument must be a scalar integer\n")
return()
}
linkablefile <- paste(dfile, ".nlinkable", sep="")
cat(nlinkable, "\n", file = linkablefile)
}
### subset ###
subsetarg <- ""
if (!missing(subset)) {
# check data type
subset <- as.integer(subset)
if (length(subset) > 1) {
cat("The 'subset' argument must be a scalar integer\n")
return()
}
else if (subset == 0 || subset > nrow(x)) {
cat("The 'subset' argument must be >0 and <= nrows\n")
return()
}
subsetarg <- paste(" -subset ", subset, sep="")
}
args <- paste("-s -std", std, "-dev", dev)
if (subsetarg != "")
args <- paste(args, subsetarg, sep=" ")
if (!missing(display)) {
if (!is.character(display))
warning("display must be a character string")
else
args <- paste("-display", display, args)
}
if (!missing(title)) {
if (!is.character(title)) {
warning("title must be a character string")
title <- deparse(substitute(matrx))
}
}
else
title <- deparse(substitute(matrx))
args <- paste("-title", paste("'", title, "'", sep=""), args)
#
# Note to installer:
# Here you will need to specify the path to the xgobi executable
# on your system.
path <- paste("/usr/dfs/xgobi/src/")
#
command <- paste(path, "xgobi", sep="")
command <- paste(command, args)
command <- paste(command, nrow(x), ncol(x),
search()[1], dfile, "&")
cat(command, "\n")
invisible(unix(command,output.to.S=F))
}
else
cat("Matrix argument required\n")
}
|
