updated docs

.readthedocs.yaml

@@ -29,4 +29,9 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-    - requirements: man/requirements.txt
+    - requirements: man/requirements.txt
+
+steps:
+  - command: |
+      pip install -r man/requirements.txt
+      sphinx-build -b html man/_build man

man/pages/examples/primates.nw

@@ -0,0 +1 @@
+((((((Cercopithecus neglectus:0.089332,Macaca mulatta:0.086881)1:0.046493,Colobus angolensis:0.135485)1:0.086552,((Hylobates lar:0.042152,Nomascus leucogenys:0.043098)0.52:0.066886,((Gorilla gorilla:0.041841,(Homo sapiens:0.039953,Pan troglodytes:0.030598)1:0.015261)1:0.036137,Pongo abelii:0.084649)1:0.027204)1:0.064662)1:0.094920,((Lagothrix lagotricha:0.094932,Saimiri boliviensis:0.156272)1:0.011861,Chiropotes satanas:0.093527)1:0.167153)1:0.162404,Tarsius syrichta:0.291270)1:0.024775,(Lemur catta:0.238657,(Loris tardigradus:0.185772,Galago moholi:0.171305)1:0.159023)1:0.044877):0.01;

man/pages/parameters.md

@@ -1,8 +1,7 @@
-# Parameters
+# Usage and Parameters
 
 Detailed descriptions of all parameters are provided below.
 
-
 *Required*
 
 * [tree](#tree) - tree file
@@ -33,12 +32,60 @@ Detailed descriptions of all parameters are provided below.
 * [line_width](#line-width) - set line width
 * [bold](#bold) - highlight tip labels in bold
 
+The primate tree used in these examples is from the [10K trees](https://10ktrees.nunn-lab.org/) project and is illustrative only.
+
+
+
 ## Required
 ### `tree`
 (`str`, Required)
 
 Either the path to a newick formatted tree or a string containing a newick formatted tree. 
 
+e.g. 
+A string containing a newick formatted tree
+
+```
+# Store the newick data as a string
+tree = "((A:0.1,B:0.2)0.5,C:0.3)0.95:0.1;"
+
+# Generate a matplotlib figure
+f = plt.figure(figsize=(5, 5))
+
+# Add an axis
+ax = plt.subplot()
+
+# Set the axis limits
+ax.set_xlim(-1, 15)
+ax.set_ylim(-5, 11)
+
+# Visualise the tree
+results = plot_phylo.plot_phylo(tree, ax)
+
+# Save the image
+f.savefig("examples/from_string.png", bbox_inches='tight')
+
+```
+![from_string](examples/from_string.png)
+
+A file containing a newick formatted tree, such as [primates.nw](examples/primates.nw).
+
+```
+# Generate a matplotlib figure
+f = plt.figure(figsize=(8, 10))
+
+# Add an axis
+ax = plt.subplot()
+
+# Plot the tree on this axis, `examples/primates.nw` is the path to the tree
+results = plot_phylo.plot_phylo("examples/primates.nw", ax)
+
+# Save the image
+plt.savefig("examples/basic_plot.png", bbox_inches='tight')
+
+```
+![Basic Tree](./examples/basic_plot.png "Basic Tree")
+
 ### `ax`
 (`matplotlib.axes._axes.Axes`, Required)