deprecated_seasonal_flu.py 文件源码

def plot_frequencies(flu, gene, mutation=None, plot_regions=None, all_muts=False, ax=None, **kwargs):
    import seaborn as sns
    sns.set_style('whitegrid')
    cols = sns.color_palette()
    linestyles = ['-', '--', '-.', ':']
    if plot_regions is None:
        plot_regions=regions
    pivots = flu.pivots
    if ax is None:
        plt.figure()
        ax=plt.subplot(111)
    if type(mutation)==int:
        mutations = [x for x,freq in flu.mutation_frequencies[('global', gene)].iteritems()
                     if (x[0]==mutation)&(freq[0]<0.5 or all_muts)]
    elif mutation is not None:
        mutations = [mutation]
    else:
        mutations=None

    if mutations is None:
        for ri, region in enumerate(plot_regions):
            count=flu.mutation_frequency_counts[region]
            plt.plot(pivots, count, c=cols[ri%len(cols)], label=region)
    else:
        print("plotting mutations", mutations)
        for ri,region in enumerate(plot_regions):
            for mi,mut in enumerate(mutations):
                if mut in flu.mutation_frequencies[(region, gene)]:
                    freq = flu.mutation_frequencies[(region, gene)][mut]
                    err = flu.mutation_frequency_confidence[(region, gene)][mut]
                    c=cols[ri%len(cols)]
                    label_str = str(mut[0]+1)+mut[1]+', '+region
                    plot_trace(ax, pivots, freq, err, c=c,
                        ls=linestyles[mi%len(linestyles)],label=label_str, **kwargs)
                else:
                    print(mut, 'not found in region',region)
    ax.ticklabel_format(useOffset=False)
    ax.legend(loc=2)