Mercurial > repos > devteam > t2ps
changeset 1:dee81096ec71 draft
Uploaded tool help images.
| author | devteam |
|---|---|
| date | Tue, 03 Jun 2014 12:36:57 -0400 |
| parents | 9e2b9ca7f33a |
| children | 4d9910e996f7 |
| files | t2ps.tgz t2ps_autoscale.png t2ps_autoscale_tree.png t2ps_heatmap.png t2ps_ideal.png t2ps_ideal_ssp.png t2ps_missing_nodes.png t2ps_node_label.png t2ps_wrapper.xml |
| diffstat | 9 files changed, 7 insertions(+), 7 deletions(-) [+] |
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--- a/t2ps_wrapper.xml Mon Jan 27 09:28:14 2014 -0500 +++ b/t2ps_wrapper.xml Tue Jun 03 12:36:57 2014 -0400 @@ -62,14 +62,14 @@ Drawing the tree with default parameters (without changing anything in the interface) will produce this tree: -.. image:: ${static_path}/images/t2ps_ideal.png +.. image:: t2ps_ideal.png :width: 500 (for explanation of colors and numbers on the tree scroll to the bottom of this help section) 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: -.. image:: ${static_path}/images/t2ps_ideal_ssp.png +.. image:: t2ps_ideal_ssp.png :width: 1000 -------- @@ -87,7 +87,7 @@ A full tree for this dataset will look like this: -.. image:: ${static_path}/images/t2ps_missing_nodes.png +.. image:: t2ps_missing_nodes.png :width: 1000 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 @@ -98,11 +98,11 @@ 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*): -.. image:: ${static_path}/images/t2ps_autoscale.png +.. image:: t2ps_autoscale.png will produce this tree: -.. image:: ${static_path}/images/t2ps_autoscale_tree.png +.. image:: t2ps_autoscale_tree.png :width: 1000 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. @@ -113,11 +113,11 @@ 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. -.. image:: ${static_path}/images/t2ps_heatmap.png +.. image:: t2ps_heatmap.png Each node is labeled with taxonomic name and the number of tree leaves belonging to this taxonomic group: -.. image:: ${static_path}/images/t2ps_node_label.png +.. image:: t2ps_node_label.png