Updated doc for gotree ltt

docs/commands/ltt.md

@@ -0,0 +1,78 @@
+# Gotree: toolkit and api for phylogenetic tree manipulation
+
+## Commands
+
+### ltt
+
+Compute or draw lineage through time data.
+
+Two options:
+
+1) Will output data visualizable in statistical packages (R, python, etc.). Set of x,y coordinates pairs: x: time (or mutations) and y: number of lineages.
+2) If `--image <image file>`` is specified, then a ltt plot is generate in the given output file. The format of the image depends on the extension (.png, .svg, .pdf, etc. see [gonum doc](https://github.com/gonum/plot/blob/342a5cee2153b051d94ae813861f9436c5584de2/plot.go#L525C17-L525C17). Image width and height can be specified (in inch) with `--image-width` and `--image-height`.
+
+
+Example of usage:
+
+```
+gotree ltt -i tree.nw -o ltt_data.txt --image ltt_image.pdf --image-width 10 --image-height 10
+```
+
+#### Usage
+
+General command
+```
+Usage:
+  gotree ltt [flags]
+
+Flags:
+  -h, --help               help for ltt
+      --image string       LTT plot image image output file (default "none")
+      --image-height int   LTT plot image output heigh (default 4)
+      --image-width int    LTT plot image image output width (default 4)
+  -i, --input string       Input tree(s) file (default "stdin")
+  -o, --output string      LTT output file (default "stdout")
+
+Global Flags:
+      --format string   Input tree format (newick, nexus, phyloxml, or nextstrain) (default "newick")
+```
+
+#### Examples
+
+* Generate ltt data from an input tree
+
+
+```
+$ echo "(((A:1,B:1):1,C:2):3,(D:4,(E:3,((F:1.5,G:1.5):0.5,H:2):1):1):1);" | gotree draw text -w 50
+                                       +-------- A
+                             +---------|
++----------------------------|         +-------- B
+|                            |
+|                            +------------------ C
+|
+|        +-------------------------------------- D
+|        |
++--------|         +---------------------------- E
+         |         |
+         +---------|              +------------- F
+                   |         +----|
+                   +---------|    +------------- G
+                             |
+                             +------------------ H
+$ echo "(((A:1,B:1):1,C:2):3,(D:4,(E:3,((F:1.5,G:1.5):0.5,H:2):1):1):1);" | gotree ltt
+0	0.000000	2
+0	1.000000	3
+0	2.000000	4
+0	3.000000	6
+0	3.500000	7
+0	4.000000	8
+0	5.000000	0
+```
+
+* Generate ltt plot from an input tree
+
+```
+$ echo "(((A:1,B:1):1,C:2):3,(D:4,(E:3,((F:1.5,G:1.5):0.5,H:2):1):1):1);" | gotree ltt --image ltt.png --image-width 10 --image-height 10
+```
+
+![LTT Plot](ltt.svg)

docs/index.md

@@ -81,8 +81,9 @@ Command                                                            | Subcommand
 --                                                                 | topologies        | Generates all possible tree topologies
 --                                                                 | uniformtree       | Randomly generates uniform trees
 --                                                                 | yuletree          | Randomly generates Yule-Harding trees
-[graft](commands/graft.md) ([api](api/graft.md))                 |                   | Graft a tree on an input tree
+[graft](commands/graft.md) ([api](api/graft.md))                   |                   | Graft a tree on an input tree
 [labels](commands/labels.md)                                       |                   | Lists labels of tree tips
+[ltt](commands/ltt.md)                                             |                   | Draws a lineage through time plot
 [matrix](commands/matrix.md) ([api](api/matrix.md))                |                   | Prints distance matrix associated to the input tree
 [merge](commands/merge.md) ([api](api/merge.md))                   |                   | Merges two rooted trees
 [nni](commands/nni.md) ([api](api/nni.md))                   |                   | Generates all NNI neighbors from a given tree