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
|
xgvis <-
function(dmat = NULL,
edges = NULL,
pos = NULL,
rowlab = NULL,
colors = NULL,
glyphs = NULL,
erase = NULL,
lines = NULL,
linecolors = NULL,
resources = NULL,
display = NULL)
{
if (missing(edges) && missing(pos) && missing(dmat)) {
cat("One of dmat, edges, or pos must be present\n")
return()
}
tpath <- getenv("S_TMP")
if(nchar(tpath) == 0) tpath <- getenv("TEMP")
basefile <- paste(tpath, tempfile("xgvis"), sep = "/")
### distance matrix ###
if (!missing(dmat)) {
dmat <- eval(dmat)
if (sum(abs(dmat[!is.na(dmat)])) == Inf > 0) {
cat("xgvis can't handle Infs in dmat, replaced with NA\n")
dmat[dmat==Inf] <- NA
}
dfile <- paste(basefile, ".dist", sep="")
write(t(dmat), file = dfile, ncolumns = ncol(dmat))
on.exit(unlink(dfile), add=T)
}
### Edges ###
if (!missing(edges))
{
# check data type
if (!is.matrix(edges) || !is.numeric(edges) || dim(edges)[2] != 2) {
cat("The 'edges' argument must be a numeric 2-column matrix\n")
return()
}
edgesfile <- paste(basefile, ".edges", sep="")
if (nrow(edges) > 0) {
write(t(edges), file = edgesfile, ncol=2)
}
on.exit(unlink(edgesfile), add=T)
}
### position matrix ###
if (!missing(pos)) {
pos <- eval(pos)
if (sum(abs(pos[!is.na(pos)])) == Inf > 0)
{
cat("xgvis can't handle Inf in pos; replaced with NA\n")
pos[pos==Inf] <- NA
}
pfile <- paste(basefile, ".pos", sep="")
write(t(pos), file = pfile, ncolumns = ncol(pos))
on.exit(unlink(pfile), add = T)
}
### Row labels ###
if (!missing(rowlab))
# 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(basefile, ".row", sep="")
write(rowlab, file = rowfile, ncol=1)
on.exit(unlink(rowfile), add = T)
}
### 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(basefile, ".colors", sep="")
write(colors, file = colorfile, ncol=1)
on.exit(unlink(colorfile), add = T)
}
### 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(basefile, ".glyphs", sep="")
write(glyphs, file = glyphfile, ncol=1)
on.exit(unlink(glyphfile), add = T)
}
### 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(basefile, ".erase", sep="")
write(erase, file = erasefile, ncol=1)
on.exit(unlink(erasefile), add = T)
}
### 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(basefile, ".lines", sep="")
if (nrow(lines) > 0) {
write(t(lines), file = linesfile, ncol=2)
on.exit(unlink(linesfile), add = T)
}
}
### Line colors ###
if ((!missing(lines) || !missing(edges)) && !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(basefile, ".linecolors", sep="")
write(linecolors, file = linecolorfile, ncol=1)
on.exit(unlink(linecolorfile), add = T)
}
### 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(basefile, ".resources", sep="")
write(resources, file = resourcefile, ncol=1)
on.exit(unlink(resourcefile), add = T)
}
# Note to installer:
# Here you need to specify the path to the xgvis batch file/ executable
# on your system.
#
# dos example:
# xgpath <- "c:/packages/xgobi/xgvis.bat"
# unix example:
xgpath <- "/usr/dfs/xgobi/joint/src/xgvis"
command <- paste(xgpath, basefile)
cat(command, "\n")
# dos:
# invisible(dos(command, multi = F, minimized = T, output.to.S = F, translate = T))
# unix:
invisible(unix(command))
}
|
