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How to use create_line_chart method in SeleniumBase

Best Python code snippet using SeleniumBase

stats_figures.py

Source:stats_figures.py

...297    )298    A, B = utils.retrieve_data_points_from_dict_in_dict(299        data, 'aligned_reads', 'mapq_percent', False300    )301    plotting.create_line_chart(302        A,303        'Distribution of MAPQ Scores: Sample A',304        'MAPQ Score',305        'Percent of Reads',306        (0,  60, 10),307        (0, 100, 20),308        3,309        'upper left',310        outdir+'mapq_dist_sample_A.pdf'311    )312    plotting.create_line_chart(313        B,314        'Distribution of MAPQ Scores: Sample B',315        'MAPQ Score',316        'Percent of Reads',317        (0,  60, 10),318        (0, 100, 20),319        3,320        'upper left',321        outdir+'mapq_dist_sample_B.pdf'322    )323    plot_data = utils.retrieve_aligned_reads_total_only(data, True)324    plotting.create_rep_avg_plot(325        [(samp, i/1000000.) for samp, i in plot_data],326        'Number of Aligned Read Fragments',327        'Aligned Read Fragments (Millions)',328        '',329        (0, 1800, 300),330        outdir+'aligned_reads.pdf'331    )332def duplicate_rate_plots(data, outdir):333    """Make plots with duplicate read rate percentages."""334    meta = {335        'dup_report_all': {336            'key1'   : 'dup_report',337            'key2'   : 'dup_all',338            'title'  : 'Percentage of Duplicate Marked Reads',339            'xlab'   : 'Percentage of Reads',340            'ylab'   : '',341            'xlims'  : (0, 100, 10),342            'figname': outdir+'dup_all.pdf'343        },344        'dup_report_q40': {345            'key1'   : 'dup_report',346            'key2'   : 'dup_q40',347            'title'  : 'Percentage of Duplicate Marked Reads',348            'xlab'   : 'Percentage of Reads',349            'ylab'   : '',350            'xlims'  : (0, 100, 10),351            'figname': outdir+'dup_q40.pdf'352        }353    }354    for vals in meta.values():355        plot_data = utils.retrieve_single_element_data_from_dict_one_output(356            data, vals['key1'], vals['key2'], True357        )358        plotting.create_rep_avg_plot(359            plot_data,360            vals['title'],361            vals['xlab'],362            vals['ylab'],363            vals['xlims'],364            vals['figname']365        )366    return 0367def cpn_retention_plots(data, outdir):368    """Make plots with CpN retention rate percentages."""369    meta = {370        'read_rtn_a': {371            'key1'   : 'read_rtn',372            'key2'   : 'rca',373            'title'  : 'Read-averaged CpA Retention',374            'xlab'   : 'Percent Retained',375            'ylab'   : '',376            'xlims'  : (0, 5, 1),377            'figname': outdir+'read_rtn_cpa.pdf'378        },379        'read_rtn_c': {380            'key1'   : 'read_rtn',381            'key2'   : 'rcc',382            'title'  : 'Read-averaged CpC Retention',383            'xlab'   : 'Percent Retained',384            'ylab'   : '',385            'xlims'  : (0, 5, 1),386            'figname': outdir+'read_rtn_cpc.pdf'387        },388        'read_rtn_g': {389            'key1'   : 'read_rtn',390            'key2'   : 'rcg',391            'title'  : 'Read-averaged CpG Retention',392            'xlab'   : 'Percent Retained',393            'ylab'   : '',394            'xlims'  : (0, 100, 10),395            'figname': outdir+'read_rtn_cpg.pdf'396        },397        'read_rtn_t': {398            'key1'   : 'read_rtn',399            'key2'   : 'rct',400            'title'  : 'Read-averaged CpT Retention',401            'xlab'   : 'Percent Retained',402            'ylab'   : '',403            'xlims'  : (0, 5, 1),404            'figname': outdir+'read_rtn_cpt.pdf'405        },406        'base_rtn_a': {407            'key1'   : 'base_rtn',408            'key2'   : 'bca',409            'title'  : 'Base-averaged CpA Retention',410            'xlab'   : 'Percent Retained',411            'ylab'   : '',412            'xlims'  : (0, 5, 1),413            'figname': outdir+'base_rtn_cpa.pdf'414        },415        'base_rtn_c': {416            'key1'   : 'base_rtn',417            'key2'   : 'bcc',418            'title'  : 'Base-averaged CpC Retention',419            'xlab'   : 'Percent Retained',420            'ylab'   : '',421            'xlims'  : (0, 5, 1),422            'figname': outdir+'base_rtn_cpc.pdf'423        },424        'base_rtn_g': {425            'key1'   : 'base_rtn',426            'key2'   : 'bcg',427            'title'  : 'Base-averaged CpG Retention',428            'xlab'   : 'Percent Retained',429            'ylab'   : '',430            'xlims'  : (0, 100, 10),431            'figname': outdir+'base_rtn_cpg.pdf'432        },433        'base_rtn_t': {434            'key1'   : 'base_rtn',435            'key2'   : 'bct',436            'title'  : 'Base-averaged CpT Retention',437            'xlab'   : 'Percent Retained',438            'ylab'   : '',439            'xlims'  : (0, 5, 1),440            'figname': outdir+'base_rtn_cpt.pdf'441        }442    }443    for vals in meta.values():444        plot_data = utils.retrieve_single_element_data_from_dict_one_output(445            data, vals['key1'], vals['key2'], True446        )447        plotting.create_rep_avg_plot(448            plot_data,449            vals['title'],450            vals['xlab'],451            vals['ylab'],452            vals['xlims'],453            vals['figname']454        )455    return 0456def create_trinucleotide_methylation_plots(data, outdir):457    """Make plots with CpWpN retention rate percentages."""458    meta = {459        'cah_methylation_percent': {460            'key'    : 'cah_methylation_percent',461            'title'  : 'Base-averaged CpApH Retention',462            'xlab'   : 'Percent Retained',463            'ylab'   : '',464            'xlims'  : (0, 5, 1),465            'figname': outdir+'cah_meth.pdf'466        },467        'cag_methylation_percent': {468            'key'    : 'cag_methylation_percent',469            'title'  : 'Base-averaged CpApG Retention',470            'xlab'   : 'Percent Retained',471            'ylab'   : '',472            'xlims'  : (0, 5, 1),473            'figname': outdir+'cag_meth.pdf'474        },475        'cth_methylation_percent': {476            'key'    : 'cth_methylation_percent',477            'title'  : 'Base-averaged CpTpH Retention',478            'xlab'   : 'Percent Retained',479            'ylab'   : '',480            'xlims'  : (0, 5, 1),481            'figname': outdir+'cth_meth.pdf'482        },483        'ctg_methylation_percent': {484            'key'    : 'ctg_methylation_percent',485            'title'  : 'Base-averaged CpTpG Retention',486            'xlab'   : 'Percent Retained',487            'ylab'   : '',488            'xlims'  : (0, 5, 1),489            'figname': outdir+'ctg_meth.pdf'490        },491    }492    for vals in meta.values():493        plot_data = utils.retrieve_single_element_data_one_output(494            data, vals['key'], True495        )496        plotting.create_rep_avg_plot(497            plot_data,498            vals['title'],499            vals['xlab'],500            vals['ylab'],501            vals['xlims'],502            vals['figname']503        )504    return 0505def mbias_plots(data, outdir):506    """Make M-bias plots."""507    A, B = utils.retrieve_data_points_from_dict_in_dict(508        data, 'cpg_rtn_readpos', '1', False509    )510    plotting.create_line_chart(511        A,512        'Read 1 CpG Retention by Read Position: Sample A',513        'Read Position',514        'Percent Retained',515        (0, 100, 20),516        (0, 100, 20),517        3,518        'lower center',519        outdir+'r1_cpg_rtn_readpos_sample_A.pdf'520    )521    plotting.create_line_chart(522        B,523        'Read 1 CpG Retention by Read Position: Sample B',524        'Read Position',525        'Percent Retained',526        (0, 100, 20),527        (0, 100, 20),528        3,529        'lower center',530        outdir+'r1_cpg_rtn_readpos_sample_B.pdf'531    )532    A, B = utils.retrieve_data_points_from_dict_in_dict(533        data, 'cpg_rtn_readpos', '2', False534    )535    plotting.create_line_chart(536        A,537        'Read 2 CpG Retention by Read Position: Sample A',538        'Read Position',539        'Percent Retained',540        (0, 100, 20),541        (0, 100, 20),542        3,543        'lower center',544        outdir+'r2_cpg_rtn_readpos_sample_A.pdf'545    )546    plotting.create_line_chart(547        B,548        'Read 2 CpG Retention by Read Position: Sample B',549        'Read Position',550        'Percent Retained',551        (0, 100, 20),552        (0, 100, 20),553        3,554        'lower center',555        outdir+'r2_cpg_rtn_readpos_sample_B.pdf'556    )557    A, B = utils.retrieve_data_points_from_dict_in_dict(558        data, 'cph_rtn_readpos', '1', False559    )560    plotting.create_line_chart(561        A,562        'Read 1 CpH Retention by Read Position: Sample A',563        'Read Position',564        'Percent Retained',565        (0, 100, 20),566        (0, 100, 20),567        3,568        'upper left',569        outdir+'r1_cph_rtn_readpos_sample_A.pdf'570    )571    plotting.create_line_chart(572        B,573        'Read 1 CpH Retention by Read Position: Sample B',574        'Read Position',575        'Percent Retained',576        (0, 100, 20),577        (0, 100, 20),578        3,579        'upper left',580        outdir+'r1_cph_rtn_readpos_sample_B.pdf'581    )582    A, B = utils.retrieve_data_points_from_dict_in_dict(583        data, 'cph_rtn_readpos', '2', False584    )585    plotting.create_line_chart(586        A,587        'Read 2 CpH Retention by Read Position: Sample A',588        'Read Position',589        'Percent Retained',590        (0, 100, 20),591        (0, 100, 20),592        3,593        'upper left',594        outdir+'r2_cph_rtn_readpos_sample_A.pdf'595    )596    plotting.create_line_chart(597        B,598        'Read 2 CpH Retention by Read Position: Sample B',599        'Read Position',600        'Percent Retained',601        (0, 100, 20),602        (0, 100, 20),603        3,604        'upper left',605        outdir+'r2_cph_rtn_readpos_sample_B.pdf'606    )607    return 0608def create_covdist_plots(data, outdir):609    """Make coverage vs. depth plots."""610    A, B = utils.retrieve_data_points_from_dict(data, 'covdist_all_base', False)611    plotting.create_line_chart(612        A,613        'Base Cumulative Coverage: Sample A',614        'Coverage',615        'Number of Bases (Millions)',616        (0, 50, 5),617        (0, 3500, 500),618        2,619        'upper right',620        outdir+'covdist_all_base_sample_A.pdf'621    )622    plotting.create_line_chart(623        B,624        'Base Cumulative Coverage: Sample B',625        'Coverage',626        'Number of Bases (Millions)',627        (0, 50, 5),628        (0, 3500, 500),629        2,630        'upper right',631        outdir+'covdist_all_base_sample_B.pdf'632    )633    A, B = utils.retrieve_data_points_from_dict(data, 'covdist_q40_base', False)634    plotting.create_line_chart(635        A,636        'Base Cumulative Coverage: Sample A',637        'Coverage',638        'Number of Bases (Millions)',639        (0, 50, 5),640        (0, 3500, 500),641        2,642        'upper right',643        outdir+'covdist_q40_base_sample_A.pdf'644    )645    plotting.create_line_chart(646        B,647        'Base Cumulative Coverage: Sample B',648        'Coverage',649        'Number of Bases (Millions)',650        (0, 50, 5),651        (0, 3500, 500),652        2,653        'upper right',654        outdir+'covdist_q40_base_sample_B.pdf'655    )656    A, B = utils.retrieve_data_points_from_dict(data, 'covdist_all_cpg', False)657    plotting.create_line_chart(658        A,659        'CpG Cumulative Coverage: Sample A',660        'Coverage',661        'Number of CpGs (Millions)',662        (0, 50, 5),663        (0, 35, 5),664        2,665        'upper right',666        outdir+'covdist_all_cpg_sample_A.pdf'667    )668    plotting.create_line_chart(669        B,670        'CpG Cumulative Coverage: Sample B',671        'Coverage',672        'Number of CpGs (Millions)',673        (0, 50, 5),674        (0, 35, 5),675        2,676        'upper right',677        outdir+'covdist_all_cpg_sample_B.pdf'678    )679    A, B = utils.retrieve_data_points_from_dict(data, 'covdist_q40_cpg', False)680    plotting.create_line_chart(681        A,682        'CpG Cumulative Coverage: Sample A',683        'Coverage',684        'Number of CpGs (Millions)',685        (0, 50, 5),686        (0, 35, 5),687        2,688        'upper right',689        outdir+'covdist_q40_cpg_sample_A.pdf'690    )691    plotting.create_line_chart(692        B,693        'CpG Cumulative Coverage: Sample B',694        'Coverage',695        'Number of CpGs (Millions)',696        (0, 50, 5),697        (0, 35, 5),698        2,699        'upper right',700        outdir+'covdist_q40_cpg_sample_B.pdf'701    )702    return 0703def create_insert_size_plots(data, outdir):704    """Create plot of insert sizes."""705    A, B = utils.retrieve_data_points_from_dict_in_dict(706        data, 'isize_data', 'percent', False707    )708    plotting.create_line_chart(709        A,710        'Insert Size: Sample A',711        'Insert Size',712        'Percent of Mapped Reads',713        (0, 700, 100),714        (0, 1.0, 0.1),715        3,716        'upper right',717        outdir+'insert_size_sample_A.pdf',718        every=50719    )720    plotting.create_line_chart(721        B,722        'Insert Size: Sample B',723        'Insert Size',724        'Percent of Mapped Reads',725        (0, 700, 100),726        (0, 1.0, 0.1),727        3,728        'upper right',729        outdir+'insert_size_sample_B.pdf',730        every=50731    )732    return 0733def create_complexity_curve_plots(data, outdir):734    """Create plot of complexity curves."""735    A, B = utils.retrieve_data_points_from_dict(data, 'complexity_curve', False)736    plotting.create_line_chart(737        [(samp, np.array(x)/1000000., np.array(y)/1000000.) for samp, x, y in A],738        'Library Complexity: Sample A',739        'Total Reads (Millions)',740        'Unique Reads (Millions)',741        (0, 600, 100),742        (0, 500, 100),743        2,744        'upper left',745        outdir+'complexity_sample_A.pdf',746        every=50747    )748    plotting.create_line_chart(749        [(samp, np.array(x)/1000000., np.array(y)/1000000.) for samp, x, y in B],750        'Library Complexity: Sample B',751        'Total Reads (Millions)',752        'Unique Reads (Millions)',753        (0, 900, 100),754        (0, 600, 100),755        2,756        'lower right',757        outdir+'complexity_sample_B.pdf',758        every=50759    )760    return 0761def create_tex_table(data, outdir):762    """Create table with CpG regional coverages."""...

main.py

Source:main.py

...146        bar_response = create_bar_chart(details['bar_data'], BASE_PRESENTATION)147        success = success and bar_response[0]148        response = "{response}. {br}".format(response=response, br=bar_response[1])149    if 'create_line_chart' in details and details['create_line_chart'] and details['line_data']:150        line_response = create_line_chart(details['line_data'], BASE_PRESENTATION)151        success = success and line_response[0]152        response = "{response}. {lr}".format(response=response, lr=line_response[1])153    if success:154        return True, response155    else:156        return False, response157@app.route("/", methods=['POST'])158def ppt_request_handle():159    print("in ppt_request_handle")160    req = request.json161    print(req)162    with open("req_sample.json", "w") as outfile:163        json.dump(req, outfile)164    if req["req"] == "create_ppt" and req["source"].lower() == "wikipedia":165        result = create_ppt(req["title"])166        if result[0]:167            response = {168                "message": "Request successful",169                "title": result[1]170            }171            return jsonify(response), 200172    elif req["req"] == "create_ppt_count" and req["source"].lower() == "wikipedia":173        result = create_ppt_with_count(req["title"], req["count"])174        if result[0]:175            response = {176                "message": "Request successful",177                "title": result[1],178                "count": result[2],179            }180            return jsonify(response), 200181    elif req["req"] == "create_ppt_count" and req["source"].lower() == "nytimes":182        result = create_ppt_ny(req["title"], req["count"])183        if result[0]:184            response = {185                "message": "Request successful",186                "title": result[1],187                "count": result[2],188            }189            return jsonify(response), 200190    elif req["req"] == "create_team_slide":191        result = create_team_slide(req["people"])192        response = {193            "message": result[1]194        }195        if result[0]:196            return jsonify(response), 200197        else:198            return jsonify(response), 400199    elif req["req"] == "create_pie_chart":200        result = create_pie_chart(req, BASE_PRESENTATION)201        response = {202            "message": result[1]203        }204        if result[0]:205            return jsonify(response), 200206        else:207            return jsonify(response), 400208    elif req["req"] == "create_bar_chart":209        result = create_bar_chart(req, BASE_PRESENTATION)210        response = {211            "message": result[1]212        }213        if result[0]:214            return jsonify(response), 200215        else:216            return jsonify(response), 400217    elif req["req"] == "create_line_chart":218        result = create_line_chart(req, BASE_PRESENTATION)219        response = {220            "message": result[1]221        }222        if result[0]:223            return jsonify(response), 200224        else:225            return jsonify(response), 400226    elif req["req"] == "create_chart" or req["req"] == "create_charts":227        result = create_charts(req)228        response = {229            "message": result[1]230        }231        if result[0]:232            return jsonify(response), 200233        else:234            return jsonify(response), 400235    elif req["req"] == "create_org_chart":236        result = True, 'Got the request'237        response = {238            "message": result[1]239        }240        if result[0]:241            return jsonify(response), 200242        else:243            return jsonify(response), 400244    return f"Cannot process request", 400245# 'Main' function to run246if __name__ == '__main__':247    # app.run(debug=True)  # run server in debug mode248    os.chdir("/Users/vishal/Documents/Auxi/PIII-Prototype/PIII-Prototype-First")249    with open('./1.json') as json_file:250        data = json.load(json_file)251    print(data)252    create_ppt_ny(data['title'], data['count'])253    # create_ppt(data['title'])254    # try:255    #     prs = Presentation('./Final - Presentation.pptx')256    # except exc.PackageNotFoundError as err:257    #     # print(f'No presentation file: {err}')258    #     prs = Presentation('../../misc/Team_Slide_Custom.pptx')259    # create_team_slide(["chris", "john", "mike", "steve"], BASE_PRESENTATION)260    # res = create_pie_chart({261    #     'req': 'create_pie_chart',262    #     'categories': ['USA', 'Canada', 'Mexico'],263    #     'percentages': ['30', '30', '40']}, BASE_PRESENTATION264    # )265    #266    # res = create_bar_chart({267    #     'req': 'create_bar_chart',268    #     'categories': ['USA', 'Canada', 'Mexico'],269    #     'values': ['81', '45', '54']}, BASE_PRESENTATION270    # )271    #272    # res = create_line_chart({273    #     'req': 'create_line_chart',274    #     "Label": ["India", "Bangladesh"],275    #     "Value": [20, 30]}, BASE_PRESENTATION276    # )277    # req = {278    #     "req": "create_chart",279    #     "details": {280    #         "create_pie_chart": True,281    #         "pie_data": {282    #             "categories": ["Russia", "India", "Bangladesh"],283    #             "percentages": [30.0, 30.0, 40.0]284    #         },285    #         "create_bar_chart": True,286    #         "bar_data": {...

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