{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"## Plotly plot of a rectangular phylogenetic tree ##"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"In this Jupyter Notebook we illustrate how to generate the Plotly plot of a phylogram with rectangular layout."
]
},
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"from Bio import Phylo\n",
"import pandas as pd"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
""
],
"text/vnd.plotly.v1+html": [
""
]
},
"metadata": {},
"output_type": "display_data"
}
],
"source": [
"from plotly.offline import download_plotlyjs, init_notebook_mode, iplot\n",
"init_notebook_mode(connected=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Read the Zika Virus tree file in `newick` format, downloaded from [nextstrain](http://nextstrain.org/zika):"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [],
"source": [
"tree = Phylo.read('Data/nextstrain_zika_tree.new', \"newick\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The next cells contain commented lines that were typed to inspect the file structure:"
]
},
{
"cell_type": "code",
"execution_count": 4,
"metadata": {},
"outputs": [],
"source": [
"#print(tree)"
]
},
{
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"source": [
"#dir(tree)\n",
"#tree.get_terminals()"
]
},
{
"cell_type": "code",
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"#tree.count_terminals()# Counts the number of terminal (leaf) nodes within this tree."
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The functions `get_x_coordinates()`, `get_y_coordinates()` are mainly the functions with the same name \n",
"from Biopython: [https://github.com/biopython/biopython/blob/master/Bio/Phylo/_utils.py](https://github.com/biopython/biopython/blob/master/Bio/Phylo/_utils.py).\n",
"\n",
"They assign cartesian coordinates to the tree nodes."
]
},
{
"cell_type": "code",
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
"def get_x_coordinates(tree):\n",
" # Associates to each clade a x-coord.\n",
" # returns a dict {clade: x-coord}, i.e the key is a clade, and x-coord its value\n",
" \n",
" xcoords = tree.depths()\n",
" # tree.depth() maps tree clades to depths (by branch length).\n",
" # returns a dict {clade: depth} where clade runs over all Clade instances of the tree,\n",
" # and depth is the distance from root to clade\n",
" \n",
" # If there are no branch lengths, assign unit branch lengths\n",
" if not max(xcoords.values()):\n",
" xcoords = tree.depths(unit_branch_lengths=True)\n",
" return xcoords\n",
" \n",
"def get_y_coordinates(tree, dist=1.3):\n",
" # y-coordinates are multiple of dist (i*dist below); \n",
" # dist: vertical distance between two consecutive leafs; it is chosen such that to get a tree of \n",
" # reasonable height \n",
" # returns a dict {clade: y-coord}\n",
" \n",
" maxheight = tree.count_terminals()#Counts the number of tree leafs.\n",
" \n",
" ycoords = dict((leaf, maxheight - i*dist) for i, leaf in enumerate(reversed(tree.get_terminals())))\n",
" def calc_row(clade):\n",
" for subclade in clade:\n",
" if subclade not in ycoords:\n",
" calc_row(subclade)\n",
" ycoords[clade] = (ycoords[clade.clades[0]] +\n",
" ycoords[clade.clades[-1]]) / 2\n",
"\n",
" if tree.root.clades:\n",
" calc_row(tree.root)\n",
" return ycoords\n"
]
},
{
"cell_type": "code",
"execution_count": 8,
"metadata": {},
"outputs": [],
"source": [
"x_coords = get_x_coordinates(tree)\n",
"y_coords = get_y_coordinates(tree)"
]
},
{
"cell_type": "code",
"execution_count": 9,
"metadata": {},
"outputs": [],
"source": [
"def get_clade_lines(orientation='horizontal', y_curr=0, x_start=0, x_curr=0, y_bot=0, y_top=0,\n",
" line_color='rgb(25,25,25)', line_width=0.5):\n",
" # define a Plotly shape of type 'line', for each branch\n",
" \n",
" branch_line = dict(type= 'line',\n",
" layer='below',\n",
" line=dict(color=line_color, \n",
" width=line_width)\n",
" )\n",
" if orientation == 'horizontal':\n",
" branch_line.update(x0=x_start,\n",
" y0=y_curr,\n",
" x1=x_curr,\n",
" y1=y_curr)\n",
" elif orientation == 'vertical':\n",
" branch_line.update(x0=x_curr,\n",
" y0=y_bot,\n",
" x1=x_curr,\n",
" y1=y_top)\n",
" else:\n",
" raise ValueError(\"Line type can be 'horizontal' or 'vertical'\")\n",
" \n",
" return branch_line \n",
" \n",
" \n",
"\n",
"def draw_clade(clade, x_start, line_shapes, line_color='rgb(15,15,15)', line_width=1):\n",
" # defines recursively the tree lines (branches), starting from the argument clade\n",
" \n",
" x_curr = x_coords[clade]\n",
" y_curr = y_coords[clade]\n",
" \n",
" # Draw a horizontal line \n",
" branch_line=get_clade_lines(orientation='horizontal', y_curr=y_curr, x_start=x_start, x_curr=x_curr, \n",
" line_color=line_color, line_width=line_width)\n",
" \n",
" line_shapes.append(branch_line)\n",
" \n",
" if clade.clades:\n",
" # Draw a vertical line connecting all children\n",
" y_top = y_coords[clade.clades[0]]\n",
" y_bot = y_coords[clade.clades[-1]]\n",
" \n",
" line_shapes.append(get_clade_lines(orientation='vertical', x_curr=x_curr, y_bot=y_bot, y_top=y_top,\n",
" line_color=line_color, line_width=line_width))\n",
" \n",
" # Draw descendants\n",
" for child in clade:\n",
" draw_clade(child, x_curr, line_shapes)\n",
" \n",
" "
]
},
{
"cell_type": "code",
"execution_count": 10,
"metadata": {},
"outputs": [],
"source": [
"line_shapes = [] \n",
"draw_clade(tree.root, 0, line_shapes, line_color='rgb(25,25,25)', line_width=1)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Get the node coordinates:"
]
},
{
"cell_type": "code",
"execution_count": 11,
"metadata": {},
"outputs": [],
"source": [
"my_tree_clades = x_coords.keys()\n",
"X = [] # list of nodes x-coordinates\n",
"Y = [] # list of nodes y-coords\n",
"text = [] #list of text to be displayed on hover over nodes\n",
"\n",
"for cl in my_tree_clades:\n",
" X.append(x_coords[cl])\n",
" Y.append(y_coords[cl])\n",
" text.append(cl.name)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Read the metatadata file to record more info about nodes:"
]
},
{
"cell_type": "code",
"execution_count": 12,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"Index(['Strain', 'Accession', 'Date', 'Region', 'Country', 'Division',\n",
" 'Authors', 'Journal', 'Title', 'Url', 'Num Date', 'Db', 'Raw Date'],\n",
" dtype='object')"
]
},
"execution_count": 12,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"df = pd.read_csv('Data/nextstrain_zika_metadata.csv')\n",
"df.columns"
]
},
{
"cell_type": "code",
"execution_count": 13,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"377"
]
},
"execution_count": 13,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"len(df)"
]
},
{
"cell_type": "code",
"execution_count": 14,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'China',\n",
" 'Japan Korea',\n",
" 'North America',\n",
" 'Oceania',\n",
" 'South America',\n",
" 'Southeast Asia'}"
]
},
"execution_count": 14,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"set(list(df['Region']))"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Set the intermediate node color:"
]
},
{
"cell_type": "code",
"execution_count": 15,
"metadata": {},
"outputs": [],
"source": [
"intermediate_node_color = 'rgb(100,100,100)'"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Set the node colors depending on region (continent):"
]
},
{
"cell_type": "code",
"execution_count": 16,
"metadata": {},
"outputs": [],
"source": [
"# North Amer.\n",
"NA_color = {'Cuba': 'rgb(252, 196, 174)',\n",
" 'Dominican Republic': 'rgb(201, 32, 32)',\n",
" 'El Salvador': 'rgb(253, 202, 181)',\n",
" 'Guadeloupe': 'rgb(253, 202, 181)',\n",
" 'Guatemala': 'rgb(252, 190, 167)',\n",
" 'Haiti': 'rgb(252, 145, 114)',\n",
" 'Honduras': 'rgb(239, 66, 49)',\n",
" 'Jamaica': 'rgb(252, 185, 161)',\n",
" 'Martinique': 'rgb(252, 190, 167)',\n",
" 'Mexico': 'rgb(247, 109, 82)',\n",
" 'Nicaragua': 'rgb(249, 121, 92)',\n",
" 'Panama': 'rgb(252, 185, 161)',\n",
" 'Puerto Rico': 'rgb(252, 174, 148)',\n",
" 'Saint Barthelemy': 'rgb(253, 202, 181)',\n",
" 'USA': 'rgb(188, 20, 26)',\n",
" 'USVI': 'rgb(206, 36, 34)'}\n",
"\n",
"\n",
"\n",
"# South Amer.\n",
"SAmer_color = {'Brazil': 'rgb(21, 127, 59)',\n",
" 'Colombia': 'rgb(153, 213, 149)',\n",
" 'Ecuador': 'rgb(208, 237, 202)',\n",
" 'French Guiana': 'rgb(211, 238, 205)',\n",
" 'Peru': 'rgb(208, 237, 202)',\n",
" 'Suriname': 'rgb(206, 236, 200)',\n",
" 'Venezuela': 'rgb(202, 234, 196)'}\n",
"\n",
"# South Asia\n",
"SAsia_color = {'Singapore': '#0000EE', 'Vietnam': '#1E90FF'}\n",
"pl_SAsia = [[0.0, '#1E90FF'], \n",
" [0.5, '#1E90FF'], \n",
" [0.5, '#0000EE'], \n",
" [1.0,'#0000EE' ]]\n",
"\n",
"\n",
"Oceania_color = {'American Samoa': 'rgb(209,95,238)',\n",
" 'Fiji': 'rgb(238,130, 238)',\n",
" 'French Polynesia': 'rgb(148,0,211)',\n",
" 'Tonga': 'rgb(238,130, 238)'}\n",
"\n",
"\n",
"China_color={'China': 'rgb(255,185,15'} \n",
"\n",
"JapanKorea_color={'Japan': '#fcdd04'}"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Assign color to nodes according to region and country:"
]
},
{
"cell_type": "code",
"execution_count": 17,
"metadata": {},
"outputs": [],
"source": [
"country=[]\n",
"region=[]\n",
"color=[intermediate_node_color]*len(X)\n",
"\n",
"for k, strain in enumerate(df['Strain']):\n",
" \n",
" i=text.index(strain)\n",
" text[i]=text[i]+f\"
Country: {df.loc[k, 'Country']}\\\n",
"
Region: {df.loc[k, 'Region']}\\\n",
"
Collection date: {df.loc[k,'Date']}\\\n",
"
Journal: {df.loc[k, 'Journal']}\\\n",
"
Authors: {df.loc[k, 'Authors']}\"\n",
" country.append(df.loc[k, 'Country'])\n",
" region.append(df.loc[k, 'Region'])\n",
" if df.loc[k, 'Region'] == 'North America':\n",
" color[i] = NA_color[df.loc[k, 'Country']]\n",
" elif df.loc[k, 'Region'] == 'South America':\n",
" color[i] = SAmer_color[df.loc[k, 'Country']] \n",
" elif df.loc[k, 'Region'] == 'Southeast Asia':\n",
" color[i] = SAsia_color[df.loc[k, 'Country']]\n",
" elif df.loc[k, 'Region'] == 'Oceania':\n",
" color[i] = Oceania_color[df.loc[k, 'Country']] \n",
" elif df.loc[k, 'Region'] == 'China':\n",
" color[i] = '#fecc00'\n",
" elif df.loc[k, 'Region'] == 'Japan Korea':\n",
" color[i]= '#dc7928'\n",
" else: pass"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Define the Plotly trace for the tree nodes:"
]
},
{
"cell_type": "code",
"execution_count": 18,
"metadata": {},
"outputs": [],
"source": [
"nodes = dict(type='scatter',\n",
" x=X,\n",
" y=Y,\n",
" mode='markers',\n",
" marker=dict(color=color, \n",
" size=5),\n",
" opacity=1.0,\n",
" text=text,\n",
" hoverinfo='text')"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"The branches are already defined and stored as Plotly shapes that are included in the plot layout below:"
]
},
{
"cell_type": "code",
"execution_count": 20,
"metadata": {},
"outputs": [],
"source": [
"layout=dict(title='Phylogeny of Zika Virus
377 genomes colored according to region and country',\n",
" font=dict(family='Balto',size=14),\n",
" width=1000,\n",
" height=3000,\n",
" autosize=False,\n",
" showlegend=False,\n",
" xaxis=dict(showline=True, \n",
" zeroline=False,\n",
" showgrid=False,\n",
" ticklen=4, \n",
" showticklabels=True,\n",
" title='branch length'),\n",
" yaxis=dict(visible=False), \n",
" hovermode='closest',\n",
" plot_bgcolor='rgb(250,250,250)',\n",
" margin=dict(l=10),\n",
" shapes=line_shapes # lines for tree branches\n",
" )"
]
},
{
"cell_type": "code",
"execution_count": 21,
"metadata": {
"scrolled": false
},
"outputs": [
{
"data": {
"application/vnd.plotly.v1+json": {
"data": [
{
"hoverinfo": "text",
"marker": {
"color": [
"rgb(100,100,100)",
"rgb(100,100,100)",
"#1E90FF",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"rgb(100,100,100)",
"#0000EE",
"#0000EE",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(238,130, 238)",
"rgb(238,130, 238)",
"rgb(100,100,100)",
"rgb(209,95,238)",
"rgb(100,100,100)",
"rgb(209,95,238)",
"rgb(100,100,100)",
"rgb(209,95,238)",
"rgb(100,100,100)",
"rgb(209,95,238)",
"rgb(209,95,238)",
"rgb(100,100,100)",
"#fecc00",
"#fecc00",
"rgb(209,95,238)",
"rgb(100,100,100)",
"rgb(209,95,238)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"#fecc00",
"#fecc00",
"rgb(100,100,100)",
"rgb(209,95,238)",
"rgb(209,95,238)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(148,0,211)",
"rgb(148,0,211)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(21, 127, 59)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
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"rgb(100,100,100)",
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"rgb(21, 127, 59)",
"rgb(100,100,100)",
"#0000EE",
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"rgb(100,100,100)",
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"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(208, 237, 202)",
"rgb(208, 237, 202)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(253, 202, 181)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(21, 127, 59)",
"rgb(21, 127, 59)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(253, 202, 181)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(252, 145, 114)",
"rgb(252, 145, 114)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(252, 145, 114)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(252, 196, 174)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(206, 36, 34)",
"rgb(206, 36, 34)",
"rgb(100,100,100)",
"rgb(206, 36, 34)",
"rgb(100,100,100)",
"rgb(206, 36, 34)",
"rgb(206, 36, 34)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"#dc7928",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(206, 36, 34)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(252, 185, 161)",
"rgb(252, 145, 114)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(188, 20, 26)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(188, 20, 26)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(188, 20, 26)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(188, 20, 26)",
"rgb(188, 20, 26)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(100,100,100)",
"rgb(201, 32, 32)",
"rgb(201, 32, 32)",
"rgb(100,100,100)",
"rgb(252, 185, 161)",
"rgb(252, 185, 161)",
"rgb(100,100,100)",
"rgb(252, 185, 161)",
"rgb(100,100,100)",
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],
"showlegend": false,
"title": "Phylogeny of Zika Virus
377 genomes colored according to region and country",
"width": 1000,
"xaxis": {
"showgrid": false,
"showline": true,
"showticklabels": true,
"ticklen": 4,
"title": "branch length",
"zeroline": false
},
"yaxis": {
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}
}
},
"text/html": [
""
],
"text/vnd.plotly.v1+html": [
""
]
},
"metadata": {},
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}
],
"source": [
"fig = dict(data=[nodes], layout=layout)\n",
"iplot(fig)#offline plot"
]
},
{
"cell_type": "code",
"execution_count": 22,
"metadata": {},
"outputs": [
{
"data": {
"text/html": [
"\n",
"\n"
],
"text/plain": [
""
]
},
"execution_count": 22,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"from IPython.core.display import HTML\n",
"def css_styling():\n",
" styles = open(\"./custom.css\", \"r\").read()\n",
" return HTML(styles)\n",
"css_styling()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.4"
}
},
"nbformat": 4,
"nbformat_minor": 2
}