plot_individual_genes.py 文件源码

def plot_profiles_to_file(annot, pntr, ups=200, smooth_param=50):
    pp = PdfPages(options.save_path + 'Figures/individual_signals.pdf')
    clrs_ = ['red', 'blue', 'black', 'orange', 'magenta', 'cyan']
    vec_sense = {}
    vec_antisense = {}
    # for qq in tq(range(annot.shape[0])):
    for qq in tq(range(100)):

        chname = annot['chr'].iloc[qq]

        if annot['strand'].iloc[qq] == '+':
            start = annot['start'].iloc[qq] - ups
            stop = annot['end'].iloc[qq]
            for key in pntr.keys():
                vec_sense[key] = pntr[key][0].get_nparray(chname, start, stop - 1)
                vec_antisense[key] = pntr[key][1].get_nparray(chname, start, stop - 1)
            xran = np.arange(start, stop)
        else:
            start = annot['start'].iloc[qq]
            stop = annot['end'].iloc[qq] + ups
            for key in pntr.keys():
                vec_sense[key] = np.flipud(pntr[key][1].get_nparray(chname, start, stop))
                vec_antisense[key] = np.flipud(pntr[key][0].get_nparray(chname, start, stop))
            xran = np.arange(stop, start, -1)

        ax = {}
        fig = pl.figure()
        pl.title(annot['name'].iloc[qq])
        for i, key in enumerate(pntr.keys()):
            sm_vec_se = sm.smooth(vec_sense[key], smooth_param)[(smooth_param - 1):-(smooth_param - 1)]
            sm_vec_as = sm.smooth(vec_antisense[key], smooth_param)[(smooth_param - 1):-(smooth_param - 1)]
            ax[key] = pl.subplot(len(pntr), 1, i+1)
            ax[key].plot(xran, vec_sense[key], label=key, color=clrs_[i], alpha=0.5)
            ax[key].plot(xran, -vec_antisense[key], color=clrs_[i], alpha=0.5)
            ax[key].plot(xran, sm_vec_se,  color=clrs_[i], linewidth=2)
            ax[key].plot(xran, -sm_vec_as, color=clrs_[i], linewidth=2)
            ax[key].legend(loc='upper center', bbox_to_anchor=(0.5, 1.05), fontsize=6, ncol=1)
        pp.savefig()

        pl.close()
    pp.close()
    for pn in pntr.values():
        pn[0].close()
        pn[1].close()