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node | parent | label | weight | |
---|---|---|---|---|
1 | 0 | Animalia | 0 | |
2 | 1 | Acanthocephala | 1330 | |
3 | 1 | Annelida | 15676 | |
4 | 1 | Arthropoda | 1114267 | |
5 | 1 | Brachiopoda | 396 | |
6 | 1 | Bryozoa | 20559 | |
7 | 1 | Chaetognatha | 132 | |
8 | 1 | Chordata | 0 | |
9 | 1 | Cnidaria | 14223 | |
10 | 1 | Ctenophora | 214 | |
11 | 1 | Dicyemida | 122 | |
12 | 1 | Echinodermata | 10684 | |
13 | 1 | Gastrotricha | 865 | |
14 | 1 | Gnathostomulida | 100 | |
15 | 1 | Hemichordata | 139 | |
16 | 1 | Kamptozoa | 173 | |
17 | 1 | Kinorhyncha | 309 | |
18 | 1 | Loricifera | 29 | |
19 | 1 | Micrognathozoa | 1 | |
20 | 1 | Mollusca | 110863 | |
21 | 1 | Nematoda | 25000 | |
22 | 1 | Nematomorpha | 356 | |
23 | 1 | Nemertea | 1356 | |
24 | 1 | Onychophora | 167 | |
25 | 1 | Orthonectida | 25 | |
26 | 1 | Phoronida | 19 | |
27 | 1 | Placozoa | 3 | |
28 | 1 | Platyhelminthes | 20575 | |
29 | 1 | Porifera | 9418 | |
30 | 1 | Priapulida | 22 | |
31 | 1 | Rotifera | 2014 | |
32 | 1 | Sipuncula | 206 | |
33 | 1 | Tardigrada | 1018 | |
34 | 1 | Xenacoelomorpha | 456 | |
35 | 8 | Actinopterygii | 32513 | |
36 | 8 | Amphibia | 8054 | |
37 | 8 | Aves | 10479 | |
38 | 8 | Cephalaspidomorphi | 47 | |
39 | 8 | Elasmobranchii | 1226 | |
40 | 8 | Holocephali | 56 | |
41 | 8 | Mammalia | 5939 | |
42 | 8 | Myxini | 82 | |
43 | 8 | Reptilia | 10233 | |
44 | 8 | Sarcopterygii | 8 | |
45 | 4 | Branchiopoda | 1 | |
46 | 4 | Cephalocarida | 1 | |
47 | 4 | Chilopoda | 1 | |
48 | 4 | Collembola | 1 | |
49 | 4 | Diplopoda | 1 | |
50 | 4 | Entognatha | 1 | |
51 | 4 | Hexanauplia | 1 | |
52 | 4 | Insecta | 0 | |
53 | 4 | Malacostraca | 34797 | |
54 | 4 | Maxillopoda | 1 | |
55 | 4 | Merostomata | 1 | |
56 | 4 | Ostracoda | 1 | |
57 | 4 | Pauropoda | 1 | |
58 | 4 | Pycnogonida | 1 | |
59 | 4 | Remipedia | 1 | |
60 | 4 | Symphyla | 1 | |
61 | 4 | Trilobita | 1 | |
62 | 4 | Arachnida | 78993 | |
63 | 52 | Archaeognatha | 1 | |
64 | 52 | Blattodea | 1 | |
65 | 52 | Caloneurodea | 1 | |
66 | 52 | Cnemidolestodea | 1 | |
67 | 52 | Coleoptera | 326344 | |
68 | 52 | Dermaptera | 1 | |
69 | 52 | Diaphanopterodea | 1 | |
70 | 52 | Diptera | 153387 | |
71 | 52 | Embioptera | 1 | |
72 | 52 | Eoblattida | 1 | |
73 | 52 | Ephemeroptera | 1 | |
74 | 52 | Glosselytrodea | 1 | |
75 | 52 | Grylloblattodea | 1 | |
76 | 52 | Hemiptera | 95396 | |
77 | 52 | Hymenoptera | 118153 | |
78 | 52 | Hypoperlida | 1 | |
79 | 52 | Lepidoptera | 149969 | |
80 | 52 | Mantodea | 1 | |
81 | 52 | Mantophasmatodea | 1 | |
82 | 52 | Mecoptera | 1 | |
83 | 52 | Megaloptera | 1 | |
84 | 52 | Meganisoptera | 1 | |
85 | 52 | Megasecoptera | 1 | |
86 | 52 | Miomoptera | 1 | |
87 | 52 | Neuroptera | 1 | |
88 | 52 | Odonata | 1 | |
89 | 52 | Orthoptera | 1 | |
90 | 52 | Palaeodictyoptera | 1 | |
91 | 52 | Paoliida | 1 | |
92 | 52 | Phasmida | 1 | |
93 | 52 | Plecoptera | 1 | |
94 | 52 | Protocoleoptera | 1 | |
95 | 52 | Protorthoptera | 1 | |
96 | 52 | Psocodea | 1 | |
97 | 52 | Raphidioptera | 1 | |
98 | 52 | Reculoidea | 1 | |
99 | 52 | Siphonaptera | 1 | |
100 | 52 | Strepsiptera | 1 | |
101 | 52 | Thysanoptera | 1 | |
102 | 52 | Titanoptera | 1 | |
103 | 52 | Trichoptera | 11513 | |
104 | 52 | Zoraptera | 1 | |
105 | 52 | Zygentoma | 1 |
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digraph { | |
rankdir=LR; | |
1[label="Animalia 0"]; | |
2[label="Chordata 0"]; | |
34[label="Arthropoda 1114267"]; | |
35[label="Insecta 0"]; | |
23[label="Acanthocephala 1330"]; | |
24[label="Nemertea 1356"]; | |
25[label="Rotifera 2014"]; | |
26[label="Porifera 9418"]; | |
27[label="4752 others"]; | |
28[label="34812 others"]; | |
29[label="1419 others"]; | |
30[label="11550 others"]; | |
31[label="Platyhelminthes 20575"]; | |
32[label="Nematoda 25000"]; | |
33[label="Mollusca 110863"]; | |
52[label="Arachnida 78993"]; | |
58[label="Mammalia 5939"]; | |
59[label="Amphibia 8054"]; | |
60[label="Reptilia 10233"]; | |
61[label="Aves 10479"]; | |
62[label="Actinopterygii 32513"]; | |
101[label="Hemiptera 95396"]; | |
102[label="Hymenoptera 118153"]; | |
103[label="Lepidoptera 149969"]; | |
104[label="Diptera 153387"]; | |
105[label="Coleoptera 326344"]; | |
1->2; | |
1->34; | |
34->35; | |
1->23; | |
1->24; | |
1->25; | |
1->26; | |
1->27; | |
34->28; | |
2->29; | |
35->30; | |
1->31; | |
1->32; | |
1->33; | |
34->52; | |
2->58; | |
2->59; | |
2->60; | |
2->61; | |
2->62; | |
35->101; | |
35->102; | |
35->103; | |
35->104; | |
35->105; | |
} | |
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library(devtools) | |
install_github("kshirley/summarytrees", build_vignettes = TRUE) | |
library(summarytrees) | |
data = read.table('/Users/rpage/Development/summarytrees/animals.csv', header=TRUE,sep=",") | |
g <- greedy(node = data[, "node"], | |
parent = data[, "parent"], | |
weight = data[, "weight"], | |
label = data[, "label"], | |
K = 30) | |
write.csv(g$summary.trees[[30]], '/Users/rpage/Development/summarytrees/summary.csv') | |
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<?php | |
//---------------------------------------------------------------------------------------- | |
// http://stackoverflow.com/a/5996888/9684 | |
function translate_quoted($string) { | |
$search = array("\\t", "\\n", "\\r"); | |
$replace = array( "\t", "\n", "\r"); | |
return str_replace($search, $replace, $string); | |
} | |
//---------------------------------------------------------------------------------------- | |
$filename = 'summary.csv'; | |
$nodes = array(); | |
$edges = array(); | |
$headings = array(); | |
$row_count = 0; | |
$file = @fopen($filename, "r") or die("couldn't open $filename"); | |
$file_handle = fopen($filename, "r"); | |
while (!feof($file_handle)) | |
{ | |
$row = fgetcsv( | |
$file_handle, | |
0, | |
translate_quoted(','), | |
translate_quoted('"') | |
); | |
$go = is_array($row); | |
if ($go) | |
{ | |
if ($row_count == 0) | |
{ | |
$headings = $row; | |
} | |
else | |
{ | |
$obj = new stdclass; | |
foreach ($row as $k => $v) | |
{ | |
if ($v != '') | |
{ | |
$obj->{$headings[$k]} = $v; | |
} | |
} | |
// print_r($obj); | |
$node_obj = new stdclass; | |
$node_obj->label = $obj->label; | |
$node_obj->weight = $obj->weight; | |
$node_obj->label .= ' '. $node_obj->weight; | |
$node_id = $obj->node; | |
if ($node_id == 'NA') | |
{ | |
$node_id = $row_count; | |
$node_obj->label = $node_obj->weight . ' others'; | |
} | |
$nodes[$node_id] = $node_obj; | |
if ($obj->parent != 0) | |
{ | |
$edges[$node_id] = $obj->parent; | |
} | |
} | |
} | |
$row_count++; | |
} | |
// print_r($nodes); | |
//print_r($edges); | |
echo "digraph {\n"; | |
echo "rankdir=LR;\n"; | |
foreach ($nodes as $id => $n) | |
{ | |
echo $id . '[label="' . addcslashes($n->label, '"') . '"];' . "\n"; | |
} | |
foreach ($edges as $n => $p) | |
{ | |
echo $p . "->" . $n . ";\n"; | |
} | |
echo "}\n"; | |
?> |
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