Commit id: 8ac2c857e0925891c1fcc68ee4e9869e4df05ccb
update add_colorbar
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103435 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -1,76 +1,151 @@ |
1 |
-A/Swine/Binh_Duong/03_08/2010 6 |
|
2 |
-A/Swine/Binh_Duong/03_10/2010 6 |
|
3 |
-A/Swine/HK/2503/2011 7 |
|
4 |
-A/Swine/HK_NS2439/2011 7 |
|
5 |
-A/Swine/GX_NS2783/2010 7 |
|
6 |
-A/Swine/GD/3767/2011 7 |
|
7 |
-A/Swine/GX/2242/2011 7 |
|
8 |
-A/Swine/GX/2803/2011 7 |
|
9 |
-A/Swine/GX_NS3106/2011 7 |
|
10 |
-A/Swine/GX_NS3108/2011 7 |
|
11 |
-A/Swine/HK_NS2810/2011 7 |
|
12 |
-A/Swine/HK/2857/2011 7 |
|
13 |
-A/Swine/HK/3238/2011 7 |
|
14 |
-A/Swine/HK/3700/2011 7 |
|
15 |
-A/Swine/HK/168/2012 7 |
|
16 |
-A/Swine/HK/459/2012 7 |
|
17 |
-A/Swine/HK/1071/2012 7 |
|
18 |
-A/Swine/HK/1284/2012 7 |
|
19 |
-A/Swine/GX/650/2012 7 |
|
20 |
-A/Swine/GX_NS1409/2012 8 |
|
21 |
-A/Swine/GD/1599/2012 6 |
|
22 |
-A/Swine/HK/2454/2012 7 |
|
23 |
-A/Swine/GX/508/2012 7 |
|
24 |
-A/Swine/HK_NS1651/2012 7 |
|
25 |
-A/Swine/HK_NS2733/2012 7 |
|
26 |
-A/Swine/HK/3280/2012 7 |
|
27 |
-A/Swine/GX_NS2394/2012 7 |
|
28 |
-A/Swine/GD_NS2701/2012 8 |
|
29 |
-A/Swine/GD_NS2892/2012 8 |
|
30 |
-A/Swine/GD/2919/2012 6 |
|
31 |
-A/Swine/HK_NS2698/2012 8 |
|
32 |
-A/Ho_Chi_Minh/459.6/2010 7 |
|
33 |
-A/Netherlands/42/2006 10 |
|
34 |
-A/Malaysia/29890/2004 11 |
|
35 |
-A/New_York/334/2004 11 |
|
36 |
-A/New_York/463/2005 11 |
|
37 |
-A/New_York/238/2005 11 |
|
38 |
-A/HaNoi/BM544/2004 10 |
|
39 |
-A/Hong_Kong/HKU39/2004 11 |
|
40 |
-A/Malaysia/29997/2004 10 |
|
41 |
-A/Western_Australia/38/2003 10 |
|
42 |
-A/Moscow/328/2003 11 |
|
43 |
-A/Hanoi/BM767/2003 12 |
|
44 |
-A/California/UR06-0589/2007 11 |
|
45 |
-A/Brisbane/09/2006 11 |
|
46 |
-A/Tokyo/Ut-Sk-1/2007 9 |
|
47 |
-A/South_Carolina/NHRC0001/2006 11 |
|
48 |
-A/Mexico/InDRE2160/2005 11 |
|
49 |
-A/Colorado/UR06-0023/2007 11 |
|
50 |
-A/Hong_Kong/NHRC0001/2005 11 |
|
51 |
-A/California/NHRC0001/2005 11 |
|
52 |
-A/Mexico/InDRE29/2006 11 |
|
53 |
-A/California/VRDL165/2009 10 |
|
54 |
-A/California/UR07-0017/2008 11 |
|
55 |
-A/Ohio/UR07-0105/2008 10 |
|
56 |
-A/Kyrgyzstan/WRAIR1255P/2008 11 |
|
57 |
-A/Thailand/CU370/2008 11 |
|
58 |
-A/Moscow/RII05/2012 11 |
|
59 |
-A/Hokkaido/30-1-a/2013 12 |
|
60 |
-A/Czech_Republic/119/2012 11 |
|
61 |
-A/Petrozavodsk/RII01/2012 11 |
|
62 |
-A/New_York/20342/2010 11 |
|
63 |
-A/Boston/DOA52/2011 11 |
|
64 |
-A/Czech_Republic/126/2012 11 |
|
65 |
-A/Singapore/H2010.559C/2010 11 |
|
66 |
-A/Auckland/615/2002 10 |
|
67 |
-A/New_York/657/1994 9 |
|
68 |
-A/Malaysia/12990/1999 11 |
|
69 |
-A/HaNoi/1766/2001 11 |
|
70 |
-A/Malaysia/10816/1999 11 |
|
71 |
-A/Netherlands/126/2001 11 |
|
72 |
-A/New_York/435/2000 11 |
|
73 |
-A/New_York/452/1999 10 |
|
74 |
-A/New_York/523/1998 10 |
|
75 |
-A/New_York/582/1996 9 |
|
76 |
-A/New_York/603/1996 9 |
|
1 |
+A/Swine/Binh_Duong/03_08/2010 5 |
|
2 |
+A/Swine/Binh_Duong/03_10/2010 5 |
|
3 |
+A/Swine/HK/2503/2011 6 |
|
4 |
+A/Swine/HK_NS2439/2011 6 |
|
5 |
+A/Swine/GX_NS2783/2010 6 |
|
6 |
+A/Swine/GD/3767/2011 6 |
|
7 |
+A/Swine/GX/2242/2011 6 |
|
8 |
+A/Swine/GX/2803/2011 6 |
|
9 |
+A/Swine/GX_NS3106/2011 6 |
|
10 |
+A/Swine/GX_NS3108/2011 6 |
|
11 |
+A/Swine/HK_NS2810/2011 6 |
|
12 |
+A/Swine/HK/2857/2011 6 |
|
13 |
+A/Swine/HK/3238/2011 6 |
|
14 |
+A/Swine/HK/3700/2011 6 |
|
15 |
+A/Swine/HK/168/2012 6 |
|
16 |
+A/Swine/HK/459/2012 6 |
|
17 |
+A/Swine/HK/1071/2012 6 |
|
18 |
+A/Swine/HK/1284/2012 6 |
|
19 |
+A/Swine/GX/650/2012 6 |
|
20 |
+A/Swine/GX_NS1409/2012 6 |
|
21 |
+A/Swine/GD/1599/2012 5 |
|
22 |
+A/Swine/HK/2454/2012 6 |
|
23 |
+A/Swine/GX/508/2012 6 |
|
24 |
+A/Swine/HK_NS1651/2012 6 |
|
25 |
+A/Swine/HK_NS2733/2012 6 |
|
26 |
+A/Swine/HK/3280/2012 6 |
|
27 |
+A/Swine/GX_NS2394/2012 6 |
|
28 |
+A/Swine/GD_NS2701/2012 6 |
|
29 |
+A/Swine/GD_NS2892/2012 6 |
|
30 |
+A/Swine/GD/2919/2012 5 |
|
31 |
+A/Swine/HK_NS2698/2012 6 |
|
32 |
+A/Ho_Chi_Minh/459.6/2010 6 |
|
33 |
+A/Netherlands/42/2006 8 |
|
34 |
+A/Malaysia/29890/2004 9 |
|
35 |
+A/New_York/334/2004 9 |
|
36 |
+A/New_York/463/2005 9 |
|
37 |
+A/New_York/238/2005 9 |
|
38 |
+A/HaNoi/BM544/2004 8 |
|
39 |
+A/Hong_Kong/HKU39/2004 9 |
|
40 |
+A/Malaysia/29997/2004 8 |
|
41 |
+A/Western_Australia/38/2003 8 |
|
42 |
+A/Moscow/328/2003 9 |
|
43 |
+A/Hanoi/BM767/2003 9 |
|
44 |
+A/California/UR06-0589/2007 9 |
|
45 |
+A/Brisbane/09/2006 9 |
|
46 |
+A/Tokyo/Ut-Sk-1/2007 7 |
|
47 |
+A/South_Carolina/NHRC0001/2006 9 |
|
48 |
+A/Mexico/InDRE2160/2005 9 |
|
49 |
+A/Colorado/UR06-0023/2007 9 |
|
50 |
+A/Hong_Kong/NHRC0001/2005 9 |
|
51 |
+A/California/NHRC0001/2005 9 |
|
52 |
+A/Mexico/InDRE29/2006 9 |
|
53 |
+A/California/VRDL165/2009 8 |
|
54 |
+A/California/UR07-0017/2008 9 |
|
55 |
+A/Ohio/UR07-0105/2008 8 |
|
56 |
+A/Kyrgyzstan/WRAIR1255P/2008 9 |
|
57 |
+A/Thailand/CU370/2008 9 |
|
58 |
+A/Moscow/RII05/2012 8 |
|
59 |
+A/Hokkaido/30-1-a/2013 8 |
|
60 |
+A/Czech_Republic/119/2012 8 |
|
61 |
+A/Petrozavodsk/RII01/2012 8 |
|
62 |
+A/New_York/20342/2010 9 |
|
63 |
+A/Boston/DOA52/2011 9 |
|
64 |
+A/Czech_Republic/126/2012 9 |
|
65 |
+A/Singapore/H2010.559C/2010 9 |
|
66 |
+A/Auckland/615/2002 8 |
|
67 |
+A/New_York/657/1994 7 |
|
68 |
+A/Malaysia/12990/1999 9 |
|
69 |
+A/HaNoi/1766/2001 9 |
|
70 |
+A/Malaysia/10816/1999 9 |
|
71 |
+A/Netherlands/126/2001 10 |
|
72 |
+A/New_York/435/2000 9 |
|
73 |
+A/New_York/452/1999 8 |
|
74 |
+A/New_York/523/1998 9 |
|
75 |
+A/New_York/582/1996 8 |
|
76 |
+A/New_York/603/1996 8 |
|
77 |
+77 8 |
|
78 |
+78 8 |
|
79 |
+79 8 |
|
80 |
+80 8 |
|
81 |
+81 8 |
|
82 |
+82 8 |
|
83 |
+83 9 |
|
84 |
+84 9 |
|
85 |
+85 9 |
|
86 |
+86 9 |
|
87 |
+87 9 |
|
88 |
+88 9 |
|
89 |
+89 9 |
|
90 |
+90 9 |
|
91 |
+91 9 |
|
92 |
+92 9 |
|
93 |
+93 9 |
|
94 |
+94 9 |
|
95 |
+95 9 |
|
96 |
+96 9 |
|
97 |
+97 9 |
|
98 |
+98 9 |
|
99 |
+99 9 |
|
100 |
+100 9 |
|
101 |
+101 9 |
|
102 |
+102 9 |
|
103 |
+103 9 |
|
104 |
+104 9 |
|
105 |
+105 9 |
|
106 |
+106 9 |
|
107 |
+107 9 |
|
108 |
+108 9 |
|
109 |
+109 9 |
|
110 |
+110 9 |
|
111 |
+111 9 |
|
112 |
+112 9 |
|
113 |
+113 9 |
|
114 |
+114 8 |
|
115 |
+115 8 |
|
116 |
+116 8 |
|
117 |
+117 9 |
|
118 |
+118 6 |
|
119 |
+119 5 |
|
120 |
+120 6 |
|
121 |
+121 6 |
|
122 |
+122 6 |
|
123 |
+123 6 |
|
124 |
+124 6 |
|
125 |
+125 6 |
|
126 |
+126 6 |
|
127 |
+127 6 |
|
128 |
+128 6 |
|
129 |
+129 6 |
|
130 |
+130 6 |
|
131 |
+131 6 |
|
132 |
+132 6 |
|
133 |
+133 6 |
|
134 |
+134 6 |
|
135 |
+135 6 |
|
136 |
+136 6 |
|
137 |
+137 6 |
|
138 |
+138 6 |
|
139 |
+139 6 |
|
140 |
+140 6 |
|
141 |
+141 6 |
|
142 |
+142 6 |
|
143 |
+143 6 |
|
144 |
+144 6 |
|
145 |
+145 6 |
|
146 |
+146 6 |
|
147 |
+147 6 |
|
148 |
+148 6 |
|
149 |
+149 9 |
|
150 |
+150 9 |
|
151 |
+151 8 |
|
77 | 152 |
\ No newline at end of file |
Commit id: 652bb7c24e092a61c71765d9ae2de1e384b1c408
update vignette to add example of merge_tree <2015-04-29, Wed>
Commit id: ac252d451f6b2e5b0d27c055e050e1e42a6ffe56
add examples folder in inst that contains sample data <2015-04-29, Wed>
Commit id: d3bb757a48866f960e5c3b5c4da088241a410deb
in addition to parsing beast time scale tree in XXX_year[\\.\\d]*, now supports XXX/year[\\.\\d]*
Commit id: 33d9f8a12db641fe8580a20e3a2b51f4798fd96f
update gplot, now rowname of heatmap will not be displayed <2015-04-28, Tue>
Commit id: 94b64487871856f3394ed53d1ab55a4b6abc0baa
add line break if substitution longer than 50 character <2015-04-28, Tue>
Commit id: 396f41d759d1eb1ffa2b8af9d1b9eda695afe110
support calculating branch for time scale tree
Commit id: 0ba9f78c1626ec0fa1c503ac8b6f50e363976586
update vignette
Commit id: 5510c5f96044238cdeca127c9514b9a02851ecdb
remove parsing tip sequence from mlb and mlc file <2015-04-28, Tue>
Commit id: fc375e2b9825d840855c6276cf4301802f3e5bdc
o remove tip.fasfile in read.paml_rst for rstfile already contains tip sequence <2015-04-28, Tue>
Commit id: 03109db58c26037aeab23dbaf372638edbad5f67
scale_color accepts user specific interval and output contains scale attribute that can be used for adding legend <2015-04-28, Tue>
Commit id: 7c5829cfa47d36db179fd8b0c089a5c4f34ff345
extend fortify methods to support additional fields <2015-04-28, Tue>
Commit id: 1b0d72edd2f8e299b56296bc6066259a682128ad
extend tree class to support additional info by merging two tree <2015-04-28, Tue>
Commit id: a8b2f5480b31e0bef233e0483966afc4ea5ef9d6
extend get.fields methods to support additional fields <2015-04-28, Tue>
Commit id: 70831ecc379dbfc6f77cd1373d3a0e03241bbf4d
implement merge_tree function to merge two tree objects into one
git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@103244 bc3139a8-67e5-0310-9ffc-ced21a209358
1 | 1 |
new file mode 100644 |
... | ... |
@@ -0,0 +1,76 @@ |
1 |
+A/Swine/Binh_Duong/03_08/2010 6 |
|
2 |
+A/Swine/Binh_Duong/03_10/2010 6 |
|
3 |
+A/Swine/HK/2503/2011 7 |
|
4 |
+A/Swine/HK_NS2439/2011 7 |
|
5 |
+A/Swine/GX_NS2783/2010 7 |
|
6 |
+A/Swine/GD/3767/2011 7 |
|
7 |
+A/Swine/GX/2242/2011 7 |
|
8 |
+A/Swine/GX/2803/2011 7 |
|
9 |
+A/Swine/GX_NS3106/2011 7 |
|
10 |
+A/Swine/GX_NS3108/2011 7 |
|
11 |
+A/Swine/HK_NS2810/2011 7 |
|
12 |
+A/Swine/HK/2857/2011 7 |
|
13 |
+A/Swine/HK/3238/2011 7 |
|
14 |
+A/Swine/HK/3700/2011 7 |
|
15 |
+A/Swine/HK/168/2012 7 |
|
16 |
+A/Swine/HK/459/2012 7 |
|
17 |
+A/Swine/HK/1071/2012 7 |
|
18 |
+A/Swine/HK/1284/2012 7 |
|
19 |
+A/Swine/GX/650/2012 7 |
|
20 |
+A/Swine/GX_NS1409/2012 8 |
|
21 |
+A/Swine/GD/1599/2012 6 |
|
22 |
+A/Swine/HK/2454/2012 7 |
|
23 |
+A/Swine/GX/508/2012 7 |
|
24 |
+A/Swine/HK_NS1651/2012 7 |
|
25 |
+A/Swine/HK_NS2733/2012 7 |
|
26 |
+A/Swine/HK/3280/2012 7 |
|
27 |
+A/Swine/GX_NS2394/2012 7 |
|
28 |
+A/Swine/GD_NS2701/2012 8 |
|
29 |
+A/Swine/GD_NS2892/2012 8 |
|
30 |
+A/Swine/GD/2919/2012 6 |
|
31 |
+A/Swine/HK_NS2698/2012 8 |
|
32 |
+A/Ho_Chi_Minh/459.6/2010 7 |
|
33 |
+A/Netherlands/42/2006 10 |
|
34 |
+A/Malaysia/29890/2004 11 |
|
35 |
+A/New_York/334/2004 11 |
|
36 |
+A/New_York/463/2005 11 |
|
37 |
+A/New_York/238/2005 11 |
|
38 |
+A/HaNoi/BM544/2004 10 |
|
39 |
+A/Hong_Kong/HKU39/2004 11 |
|
40 |
+A/Malaysia/29997/2004 10 |
|
41 |
+A/Western_Australia/38/2003 10 |
|
42 |
+A/Moscow/328/2003 11 |
|
43 |
+A/Hanoi/BM767/2003 12 |
|
44 |
+A/California/UR06-0589/2007 11 |
|
45 |
+A/Brisbane/09/2006 11 |
|
46 |
+A/Tokyo/Ut-Sk-1/2007 9 |
|
47 |
+A/South_Carolina/NHRC0001/2006 11 |
|
48 |
+A/Mexico/InDRE2160/2005 11 |
|
49 |
+A/Colorado/UR06-0023/2007 11 |
|
50 |
+A/Hong_Kong/NHRC0001/2005 11 |
|
51 |
+A/California/NHRC0001/2005 11 |
|
52 |
+A/Mexico/InDRE29/2006 11 |
|
53 |
+A/California/VRDL165/2009 10 |
|
54 |
+A/California/UR07-0017/2008 11 |
|
55 |
+A/Ohio/UR07-0105/2008 10 |
|
56 |
+A/Kyrgyzstan/WRAIR1255P/2008 11 |
|
57 |
+A/Thailand/CU370/2008 11 |
|
58 |
+A/Moscow/RII05/2012 11 |
|
59 |
+A/Hokkaido/30-1-a/2013 12 |
|
60 |
+A/Czech_Republic/119/2012 11 |
|
61 |
+A/Petrozavodsk/RII01/2012 11 |
|
62 |
+A/New_York/20342/2010 11 |
|
63 |
+A/Boston/DOA52/2011 11 |
|
64 |
+A/Czech_Republic/126/2012 11 |
|
65 |
+A/Singapore/H2010.559C/2010 11 |
|
66 |
+A/Auckland/615/2002 10 |
|
67 |
+A/New_York/657/1994 9 |
|
68 |
+A/Malaysia/12990/1999 11 |
|
69 |
+A/HaNoi/1766/2001 11 |
|
70 |
+A/Malaysia/10816/1999 11 |
|
71 |
+A/Netherlands/126/2001 11 |
|
72 |
+A/New_York/435/2000 11 |
|
73 |
+A/New_York/452/1999 10 |
|
74 |
+A/New_York/523/1998 10 |
|
75 |
+A/New_York/582/1996 9 |
|
76 |
+A/New_York/603/1996 9 |