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comparison t2ps_wrapper.xml @ 1:dee81096ec71 draft

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author devteam
date Tue, 03 Jun 2014 12:36:57 -0400
parents 9e2b9ca7f33a
children 4d9910e996f7
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0:9e2b9ca7f33a 1:dee81096ec71
60 Species_3 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3 60 Species_3 3 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum3 subphylum3 superclass3 class3 subclass3 superorder3 order3 suborder3 superfamily3 family3 subfamily3 tribe3 subtribe3 genus3 subgenus3 species3 subspecies3
61 Species_4 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4 61 Species_4 4 root superkingdom1 kingdom1 subkingdom1 superphylum1 phylum4 subphylum4 superclass4 class4 subclass4 superorder4 order4 suborder4 superfamily4 family4 subfamily4 tribe4 subtribe4 genus4 subgenus4 species4 subspecies4
62 62
63 Drawing the tree with default parameters (without changing anything in the interface) will produce this tree: 63 Drawing the tree with default parameters (without changing anything in the interface) will produce this tree:
64 64
65 .. image:: ${static_path}/images/t2ps_ideal.png 65 .. image:: t2ps_ideal.png
66 :width: 500 66 :width: 500
67 67
68 (for explanation of colors and numbers on the tree scroll to the bottom of this help section) 68 (for explanation of colors and numbers on the tree scroll to the bottom of this help section)
69 69
70 Here *Class* rank represent terminal nodes (leaves) of the tree because it is the default setting of the "*show ranks from root to*" drop-down. Changing the drop-down to "*Subspecies*" will produce this: 70 Here *Class* rank represent terminal nodes (leaves) of the tree because it is the default setting of the "*show ranks from root to*" drop-down. Changing the drop-down to "*Subspecies*" will produce this:
71 71
72 .. image:: ${static_path}/images/t2ps_ideal_ssp.png 72 .. image:: t2ps_ideal_ssp.png
73 :width: 1000 73 :width: 1000
74 74
75 -------- 75 --------
76 76
77 **Example 2: Fake data with missing nodes** 77 **Example 2: Fake data with missing nodes**
85 85
86 (here *phylum* for Species_3 and *subgenus* for Species_2 are unassigned) 86 (here *phylum* for Species_3 and *subgenus* for Species_2 are unassigned)
87 87
88 A full tree for this dataset will look like this: 88 A full tree for this dataset will look like this:
89 89
90 .. image:: ${static_path}/images/t2ps_missing_nodes.png 90 .. image:: t2ps_missing_nodes.png
91 :width: 1000 91 :width: 1000
92 92
93 Missing nodes are simply omitted from the tree (there are no gray boxes corresponding to "n") but the branch length is maintained so that taxa belonging to the same taxonomic rank are always aligned with each other 93 Missing nodes are simply omitted from the tree (there are no gray boxes corresponding to "n") but the branch length is maintained so that taxa belonging to the same taxonomic rank are always aligned with each other
94 94
95 -------- 95 --------
96 96
97 **Autoscaling the tree** 97 **Autoscaling the tree**
98 98
99 You can use the "*maximum number of leaves*" to restrict the tree to a specified number of leaves (external nodes). Using the following setting on the above dataset (note *show ranks from root to* set to *show entire tree* and *maximum number of leaves* is set *3*): 99 You can use the "*maximum number of leaves*" to restrict the tree to a specified number of leaves (external nodes). Using the following setting on the above dataset (note *show ranks from root to* set to *show entire tree* and *maximum number of leaves* is set *3*):
100 100
101 .. image:: ${static_path}/images/t2ps_autoscale.png 101 .. image:: t2ps_autoscale.png
102 102
103 will produce this tree: 103 will produce this tree:
104 104
105 .. image:: ${static_path}/images/t2ps_autoscale_tree.png 105 .. image:: t2ps_autoscale_tree.png
106 :width: 1000 106 :width: 1000
107 107
108 Here the tree is automatically trimmed at a taxonomic rank that will only have 3 outer nodes. This is very useful for initial evaluation of very large trees where you want to only see, say, 1,000 outer nodes at once. 108 Here the tree is automatically trimmed at a taxonomic rank that will only have 3 outer nodes. This is very useful for initial evaluation of very large trees where you want to only see, say, 1,000 outer nodes at once.
109 109
110 ------- 110 -------
111 111
112 **Explanation of phylogenetic tree markup** 112 **Explanation of phylogenetic tree markup**
113 113
114 Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the number of leaves it leads to and vice versa. 114 Branches of the tree are colored according to the heatmap below. The "bluer" the branch the lesser the number of leaves it leads to and vice versa.
115 115
116 .. image:: ${static_path}/images/t2ps_heatmap.png 116 .. image:: t2ps_heatmap.png
117 117
118 Each node is labeled with taxonomic name and the number of tree leaves belonging to this taxonomic group: 118 Each node is labeled with taxonomic name and the number of tree leaves belonging to this taxonomic group:
119 119
120 .. image:: ${static_path}/images/t2ps_node_label.png 120 .. image:: t2ps_node_label.png
121 121
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125 125