From 9faf7ba38780b10ab3770d47940baee10f9a7fa7 Mon Sep 17 00:00:00 2001 From: Katy Brown Date: Thu, 28 Mar 2024 16:15:53 +0000 Subject: [PATCH] updated docs --- .readthedocs.yaml | 7 +++- examples/from_string.png | Bin 0 -> 4997 bytes man/pages/examples/from_string.png | Bin 0 -> 4997 bytes man/pages/examples/primates.nw | 1 + man/pages/parameters.md | 51 +++++++++++++++++++++++++++-- 5 files changed, 56 insertions(+), 3 deletions(-) create mode 100644 examples/from_string.png create mode 100644 man/pages/examples/from_string.png create mode 100644 man/pages/examples/primates.nw diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 83579bc..4dd0439 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -29,4 +29,9 @@ sphinx: # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html python: install: - - requirements: man/requirements.txt \ No newline at end of file + - requirements: man/requirements.txt + +steps: + - command: | + pip install -r 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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; \ No newline at end of file diff --git a/man/pages/parameters.md b/man/pages/parameters.md index ff14e3c..3301175 100644 --- a/man/pages/parameters.md +++ b/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)