roary

# Roary pangenome plots¶

###### Toggle source code

In [1]:

    # Plotting imports
    %matplotlib inline

    import matplotlib.pyplot as plt
    import seaborn as sns

    sns.set_style('white')

In [2]:

    # Other imports
    import os
    import pandas as pd
    import numpy as np
    from Bio import Phylo

## parSNP tree¶

Any other valid newick file is fine, if the tip labels is the same as in the gene_presence_absence matrix from roary.

In [3]:

    t = Phylo.read('parsnp.tree', 'newick')

In [4]:

    # Max distance to create better plots
    mdist = max([t.distance(t.root, x) for x in t.get_terminals()])

## Roary¶

In [5]:

    # Load roary
    roary = pd.read_table('gene_presence_absence.csv',
                         sep=',',
                         low_memory=False)
    # Set index (group name)
    roary.set_index('Gene', inplace=True)
    # Drop the other info columns
    roary.drop(list(roary.columns[:10]), axis=1, inplace=True)

In [6]:

    # Transform it in a presence/absence matrix (1/0)
    roary.replace('.{2,100}', 1, regex=True, inplace=True)
    roary.replace(np.nan, 0, regex=True, inplace=True)

In [7]:

    # Sort the matrix by the sum of strains presence
    idx = roary.sum(axis=1).order(ascending=False).index
    roary_sorted = roary.ix[idx]

In [8]:

    # Pangenome frequency plot
    plt.figure(figsize=(7, 5))

    plt.hist(roary.sum(axis=1), roary.shape[1],
             histtype="stepfilled", alpha=.7)

    plt.xlabel('Number of genomes')
    plt.ylabel('Number of genes')

    sns.despine(left=True,
                bottom=True)

In [9]:

    # Sort the matrix according to tip labels in the tree
    roary_sorted = roary_sorted[[x.name for x in t.get_terminals()]]

In [10]:

    # PLot presence/absence matrix against the tree
    with sns.axes_style('whitegrid'):
        fig = plt.figure(figsize=(17, 10))

        ax1=plt.subplot2grid((1,40), (0, 10), colspan=30)
        a=ax1.imshow(roary_sorted.T, cmap=plt.cm.Blues,
                   vmin=0, vmax=1,
                   aspect='auto',
                   interpolation='none',
                    )
        ax1.set_yticks([])
        ax1.set_xticks([])
        ax1.axis('off')

        ax = fig.add_subplot(1,2,1)
        ax=plt.subplot2grid((1,40), (0, 0), colspan=10, axisbg='white')

        fig.subplots_adjust(wspace=0, hspace=0)

        ax1.set_title('Roary matrix\n(%d gene clusters)'%roary.shape[0])

        Phylo.draw(t, axes=ax,
                   show_confidence=False,
                   label_func=lambda x: None,
                   xticks=([],), yticks=([],),
                   ylabel=('',), xlabel=('',),
                   xlim=(-0.01,mdist+0.01),
                   axis=('off',),
                   title=('parSNP tree\n(%d strains)'%roary.shape[1],),
                  )

In [11]:

    # Plot the pangenome pie chart
    plt.figure(figsize=(10, 10))

    core = roary[roary.sum(axis=1) == roary.shape[1]].shape[0]
    softcore = roary[(roary.sum(axis=1) < roary.shape[1]) &
                     (roary.sum(axis=1) >= roary.shape[1]*0.95)].shape[0]
    shell = roary[(roary.sum(axis=1) < roary.shape[1]*0.95) &
                     (roary.sum(axis=1) >= roary.shape[1]*0.15)].shape[0]
    cloud = roary[roary.sum(axis=1) < roary.shape[1]*0.15].shape[0]

    total = roary.shape[0]

    def my_autopct(pct):
        val=int(pct*total/100.0)
        return '{v:d}'.format(v=val)

    a=plt.pie([core, softcore, shell, cloud],
          labels=['core\n(%d strains)'%roary.shape[1],
                  'soft-core\n(%d <= strains < %d)'%(roary.shape[1]*.95,
                                                     roary.shape[1]),
                  'shell\n(%d <= strains < %d)'%(roary.shape[1]*.15,
                                                 roary.shape[1]*.95),
                  'cloud\n(strains < %d)'%(roary.shape[1]*.15)],
          explode=[0.1, 0.05, 0.02, 0], radius=0.9,
          colors=[(0, 0, 1, float(x)/total) for x in (core, softcore, shell, cloud)],
          autopct=my_autopct)