Exemple #1
0
    def _get_plot_view_configs(self):
        """
        Any change to the 'raw' view of a report plot should be changed here.

        There's three histogram plots.

        1. Subread concordance
        2. Subread rendlength
        3. Readlength

        """
        _p = [
            PlotViewProperties(
                Constants.P_SUBREAD_CONCORDANCE,
                Constants.PG_SUBREAD_CONCORDANCE,
                generate_plot,
                'mapped_subread_concordance_histogram.png',
                xlabel=get_plot_xlabel(spec, Constants.PG_SUBREAD_CONCORDANCE,
                                       Constants.P_SUBREAD_CONCORDANCE),
                ylabel=get_plot_ylabel(spec, Constants.PG_SUBREAD_CONCORDANCE,
                                       Constants.P_SUBREAD_CONCORDANCE),
                color=get_green(3),
                edgecolor=get_green(2),
                use_group_thumb=True,
                plot_group_title=get_plot_title(
                    spec,
                    Constants.PG_SUBREAD_CONCORDANCE,
                    Constants.P_SUBREAD_CONCORDANCE)),
            PlotViewProperties(
                Constants.P_SUBREAD_LENGTH,
                Constants.PG_SUBREAD_LENGTH,
                generate_plot,
                'mapped_subreadlength_histogram.png',
                xlabel=get_plot_xlabel(spec, Constants.PG_SUBREAD_LENGTH,
                                       Constants.P_SUBREAD_LENGTH),
                ylabel=get_plot_ylabel(spec, Constants.PG_SUBREAD_LENGTH,
                                       Constants.P_SUBREAD_LENGTH),
                use_group_thumb=True,
                color=get_blue(3),
                edgecolor=get_blue(2),
                plot_group_title=get_plot_title(spec,
                                                Constants.PG_SUBREAD_LENGTH,
                                                Constants.P_SUBREAD_LENGTH)),
            PlotViewProperties(
                Constants.P_READLENGTH,
                Constants.PG_READLENGTH,
                generate_plot,
                'mapped_readlength_histogram.png',
                xlabel=get_plot_xlabel(spec, Constants.PG_READLENGTH,
                                       Constants.P_READLENGTH),
                ylabel=get_plot_ylabel(spec, Constants.PG_READLENGTH,
                                       Constants.P_READLENGTH),
                color=get_blue(3),
                edgecolor=get_blue(2),
                use_group_thumb=True,
                plot_group_title=get_plot_title(spec, Constants.PG_READLENGTH,
                                                Constants.P_READLENGTH)),
        ]
        return {v.plot_id: v for v in _p}
Exemple #2
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    def _get_plot_view_configs(self):
        """
        Any change to the 'raw' view of a report plot should be changed here.

        There's three histogram plots.

        1. Subread concordance
        2. Subread rendlength
        3. Readlength

        """
        _p = [
            PlotViewProperties(
                Constants.P_SUBREAD_CONCORDANCE,
                Constants.PG_SUBREAD_CONCORDANCE,
                generate_plot,
                'mapped_subread_concordance_histogram.png',
                xlabel=get_plot_xlabel(spec, Constants.PG_SUBREAD_CONCORDANCE,
                                       Constants.P_SUBREAD_CONCORDANCE),
                ylabel=get_plot_ylabel(spec, Constants.PG_SUBREAD_CONCORDANCE,
                                       Constants.P_SUBREAD_CONCORDANCE),
                color=get_green(3),
                edgecolor=get_green(2),
                use_group_thumb=True,
                plot_group_title=get_plot_title(
                    spec,
                    Constants.PG_SUBREAD_CONCORDANCE,
                    Constants.P_SUBREAD_CONCORDANCE)),
            PlotViewProperties(
                Constants.P_SUBREAD_LENGTH,
                Constants.PG_SUBREAD_LENGTH,
                generate_plot,
                'mapped_subreadlength_histogram.png',
                xlabel=get_plot_xlabel(spec, Constants.PG_SUBREAD_LENGTH,
                                       Constants.P_SUBREAD_LENGTH),
                ylabel=get_plot_ylabel(spec, Constants.PG_SUBREAD_LENGTH,
                                       Constants.P_SUBREAD_LENGTH),
                use_group_thumb=True,
                color=get_blue(3),
                edgecolor=get_blue(2),
                plot_group_title=get_plot_title(spec,
                                                Constants.PG_SUBREAD_LENGTH,
                                                Constants.P_SUBREAD_LENGTH)),
            PlotViewProperties(
                Constants.P_READLENGTH,
                Constants.PG_READLENGTH,
                generate_plot,
                'mapped_readlength_histogram.png',
                xlabel=get_plot_xlabel(spec, Constants.PG_READLENGTH,
                                       Constants.P_READLENGTH),
                ylabel=get_plot_ylabel(spec, Constants.PG_READLENGTH,
                                       Constants.P_READLENGTH),
                color=get_blue(3),
                edgecolor=get_blue(2),
                use_group_thumb=True,
                plot_group_title=get_plot_title(spec, Constants.PG_READLENGTH,
                                                Constants.P_READLENGTH)),
        ]
        return {v.plot_id: v for v in _p}
Exemple #3
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def _plot_view_configs():
    """
    Any change to the 'raw' view of a report plot should be changed here.
    """

    _p = [PlotViewProperties(Constants.P_PRE_FILTER_READ_LENGTH_HIST,
                             Constants.PG_READ_LENGTH,
                             custom_read_length_histogram,
                             Constants.I_PRE_FILTER_READ_LENGTH,
                             xlabel="ReadLength",
                             ylabel="Reads",
                             rlabel="bp > Read Length",
                             title="Pre-Filter",
                             color=get_green(3),
                             edgecolor=get_green(2),
                             plot_group_title="Polymerase Read Length"),
          PlotViewProperties(Constants.P_POST_FILTER_READ_LENGHT_HIST,
                             Constants.PG_READ_LENGTH,
                             custom_read_length_histogram,
                             Constants.I_POST_FILTER_READ_LENGTH,
                             xlabel="ReadLength",
                             ylabel="Reads",
                             rlabel="bp > Read Length",
                             title="Post-Filter",
                             color=get_green(3),
                             edgecolor=get_green(2),
                             use_group_thumb=True,
                             plot_group_title="Polymerase Read Length"),
          PlotViewProperties(Constants.P_PRE_FILTER_READ_SCORE_HIST,
                             Constants.PG_READ_SCORE,
                             custom_read_accuracy_histogram,
                             Constants.I_PRE_FILTER_READ_SCORE,
                             xlabel="Read Quality",
                             ylabel="Reads",
                             rlabel="bp > Read Quality",
                             title="Pre-Filter",
                             color=get_blue(3),
                             edgecolor=get_blue(2),
                             plot_group_title="Polymerase Read Quality"),
          PlotViewProperties(Constants.P_POST_FILTER_READ_SCORE_HIST,
                             Constants.PG_READ_SCORE,
                             custom_read_accuracy_histogram,
                             Constants.I_POST_FILTER_READ_SCORE,
                             xlabel="Read Quality",
                             ylabel="Reads",
                             rlabel="bp > Read Quality",
                             title="Post-Filter",
                             color=get_blue(3),
                             edgecolor=get_blue(2),
                             use_group_thumb=True,
                             plot_group_title="Polymerase Read Quality")
          ]

    # make it easier to access
    return {v.plot_id: v for v in _p}
Exemple #4
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 def _get_plot_view_configs(self):
     """
     Any change to the 'raw' view of a report plot should be changed here.
 
     There's three histogram plots.
 
     1. Subread accuracy
     2. Subread rendlength
     3. Readlength
 
     """
     _p = [
         PlotViewProperties(
             Constants.P_SUBREAD_ACCURACY,
             Constants.PG_SUBREAD_ACCURACY,
             generate_plot,
             'mapped_subread_accuracy_histogram.png',
             xlabel="Concordance",
             ylabel="Subreads",
             color=get_green(3),
             edgecolor=get_green(2),
             use_group_thumb=True,
             plot_group_title="Mapped Subread Accuracy"),
         PlotViewProperties(
             Constants.P_SUBREAD_LENGTH,
             Constants.PG_SUBREAD_LENGTH,
             generate_plot,
             'mapped_subreadlength_histogram.png',
             xlabel="Subread Length",
             ylabel="Subreads",
             use_group_thumb=True,
             color=get_blue(3),
             edgecolor=get_blue(2),
             plot_group_title="Mapped Subread Length"),
         PlotViewProperties(
             Constants.P_READLENGTH,
             Constants.PG_READLENGTH,
             generate_plot,
             'mapped_readlength_histogram.png',
             xlabel="Read Length",
             ylabel="Reads",
             color=get_blue(3),
             edgecolor=get_blue(2),
             use_group_thumb=True,
             plot_group_title="Mapped Polymerase Read Length")
     ]
     return {v.plot_id: v for v in _p}
Exemple #5
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def make_nreads_histogram(bc_groups, base_dir):
    """
    Create simple histogram of read count frequency per barcode.
    """
    fig, ax = make_histogram(
        datum=[float(g.n_reads) for g in bc_groups],  # FIXME workaround
        axis_labels=["Number of Reads", "Number of Barcoded Samples"],
        nbins=min(len(bc_groups), 20),
        barcolor=get_blue(3))
    return _to_plot(fig, Constants.P_HIST_NREADS, base_dir)
Exemple #6
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def make_readlength_histogram(bc_groups, base_dir):
    """
    Create simple histogram of read length frequency per barcode.
    """
    fig, ax = make_histogram(
        datum=[float(g.mean_read_length()) for g in bc_groups],  # FIXME
        axis_labels=["Mean Read Length", "Number of Barcoded Samples"],
        nbins=min(len(bc_groups), 20),
        barcolor=get_blue(3))
    return _to_plot(fig, Constants.P_HIST_RL, base_dir)
Exemple #7
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def _create_bars(contig_variants):
    """
    :param contig_variants: (ContigVariants)
    :returns: tuple of pbreports.plot.helper.Bar objects
    """

    dataIns = np.array([l[1] for l in contig_variants.variants])
    dataDels = np.array([l[2] for l in contig_variants.variants])
    dataSnv = np.array([l[3] for l in contig_variants.variants])

    insBarModel = PH.Bar(dataIns, 'Insertions', color=PH.get_blue(3))
    delBarModel = PH.Bar(dataDels, 'Deletions', color=PH.get_green(3))
    snvBarModel = PH.Bar(dataSnv, 'Substitutions', color=PH.get_orange())

    return (insBarModel, delBarModel, snvBarModel)
Exemple #8
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def make_bcqual_histogram(bc_groups, base_dir):
    """
    Create simple histogram of barcode quality score frequency over all
    barcoded subreads.
    """
    data = []
    for g in bc_groups:
        data.extend(g.bqs)
    fig, ax = make_histogram(
        datum=data,
        axis_labels=["Barcode Quality Score", "Number of Barcoded Subreads"],
        nbins=50,
        barcolor=get_blue(3))
    ax.axvline(26, color='r')
    return _to_plot(fig, Constants.P_HIST_BQ, base_dir)
Exemple #9
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_custom_read_accuracy_histogram = functools.partial(
    _custom_histogram_with_cdf,
    meta_rpt.get_meta_plotgroup(Constants.PG_ACCURACY).get_meta_plot(
        Constants.P_ACCURACY).ylabel["Custom"], 1000000)

# These functions need to generate a function with signature (data,
# output_dir, dpi=)
create_readlength_plot = functools.partial(
    create_plot, _custom_read_length_histogram, Constants.P_READLENGTH,
    (meta_rpt.get_meta_plotgroup(Constants.PG_READLENGTH).get_meta_plot(
        Constants.P_READLENGTH).xlabel,
     meta_rpt.get_meta_plotgroup(Constants.PG_READLENGTH).get_meta_plot(
         Constants.P_READLENGTH).ylabel["L"],
     meta_rpt.get_meta_plotgroup(Constants.PG_READLENGTH).get_meta_plot(
         Constants.P_READLENGTH).ylabel["R"]), 80,
    Constants.I_CCS_READ_LENGTH_HIST, get_blue(3))

create_accuracy_plot = functools.partial(
    create_plot, _custom_read_accuracy_histogram, Constants.P_ACCURACY,
    (meta_rpt.get_meta_plotgroup(Constants.PG_ACCURACY).get_meta_plot(
        Constants.P_ACCURACY).xlabel,
     meta_rpt.get_meta_plotgroup(Constants.PG_ACCURACY).get_meta_plot(
         Constants.P_ACCURACY).ylabel["L"],
     meta_rpt.get_meta_plotgroup(Constants.PG_ACCURACY).get_meta_plot(
         Constants.P_ACCURACY).ylabel["R"]), 80,
    Constants.I_CCS_READ_ACCURACY_HIST, get_green(3))

create_npasses_plot = functools.partial(
    create_plot, _make_histogram, Constants.P_NPASSES,
    (meta_rpt.get_meta_plotgroup(Constants.PG_NPASSES).get_meta_plot(
        Constants.P_NPASSES).xlabel,
    fig.savefig(path, dpi=dpi)
    log.debug("Saved plot with id {i} to {p}".format(p=path, i=plot_id))
    thumbnail = plot_name.replace(".png", "_thumb.png")

    fig.savefig(os.path.join(output_dir, thumbnail), dpi=20)
    plt.close(fig)
    log.debug("Saved plot to {p}".format(p=thumbnail))
    plot = Plot(plot_id, os.path.basename(plot_name),
                thumbnail=os.path.basename(thumbnail))

    return plot

create_readlength_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_READLENGTH,
    ("Read Length", "Reads", "Reads > Read Length"), 80,
    "consensus_isoforms_readlength_hist.png", get_blue(3))


def makeReport(inReadsFN, inSummaryFN, outDir):
    """
    Generate a report with ID, tables, attributes and plot groups.

    inReadsFN --- an input FASTA file which has all consensus
    isoforms produced by pbtranscript.py cluster.
    This file is required to plot a read length histogram as part of
    the report:
         consensus_isoforms_readlength_hist.png

    inSummaryFN --- a summary TXT file with cluster attributes,
    including two attributes:
         number of consensus isoforms
Exemple #11
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    log.debug("Saved plot to {p}".format(p=thumbnail))
    plot = Plot(plot_id, to_b(plot_name), thumbnail=to_b(thumbnail))

    return plot

# These functions create signatures (datum, axis_labels, nbins, barcolor
_custom_read_length_histogram = functools.partial(
    _custom_histogram_with_cdf, "Mb > Read Length", 1000000)
_custom_read_accuracy_histogram = functools.partial(
    _custom_histogram_with_cdf, "Mb > Predicted Accuracy", 1000000)


# These functions need to generate a function with signature (datum,
# output_dir, dpi=)
create_readlength_plot = functools.partial(__create_plot, _custom_read_length_histogram, Constants.P_READLENGTH,
                                           ("Read Length", "Reads", "bp > Read Length"), 80, Constants.I_CCS_READ_LENGTH_HIST, get_blue(3))

create_accuracy_plot = functools.partial(__create_plot, _custom_read_accuracy_histogram, Constants.P_ACCURACY,
                                         ("Quality", "Reads", "bp > Predicted Accuracy"), 80, Constants.I_CCS_READ_ACCURACY_HIST, get_green(3))

create_npasses_plot = functools.partial(__create_plot, _make_histogram, Constants.P_NPASSES,
                                        ("Number of Passes", "Reads"), 80, Constants.I_CCS_NUM_PASSES_HIST, "#F18B17")

create_scatter_plot = functools.partial(__create_plot,
                                        scatter_plot_accuracy_vs_numpasses, Constants.P_SCATTER,
                                        ("Number of passes",
                                         "Predicted accuracy (Phred QV)"), None,
                                        Constants.I_CCS_SCATTER_PLOT, get_blue(3))


def to_report(ccs_subread_set, output_dir):
Exemple #12
0
    fig.savefig(path, dpi=dpi)
    log.debug("Saved plot with id {i} to {p}".format(p=path, i=plot_id))
    thumbnail = plot_name.replace(".png", "_thumb.png")

    fig.savefig(os.path.join(output_dir, thumbnail), dpi=20)
    plt.close(fig)
    log.debug("Saved plot to {p}".format(p=thumbnail))
    plot = Plot(plot_id, os.path.basename(plot_name),
                thumbnail=os.path.basename(thumbnail))

    return plot

create_readlength_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_READLENGTH,
    ("Read Length", "Reads", "Reads > Read Length"), 80,
    "consensus_isoforms_readlength_hist.png", get_blue(3))

create_avgqv_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_AVGQV,
    ("HQ LQ Isoform Average QV", "Isoforms", "Isoforms > Average QV"), 80,
    "hq_lq_isoforms_avgqv_hist.png", get_blue(3))


def makeReport(inReadsFN, hq_isoforms_fq, lq_isoforms_fq, inSummaryFN, outDir):
    """
    Generate a report with ID, tables, attributes and plot groups.

    inReadsFN --- an input FASTA file which has all consensus
    isoforms produced by pbtranscript.py cluster.
    This file is required to plot a read length histogram as part of
    the report:
Exemple #13
0
    fig.savefig(path, dpi=dpi)
    log.debug("Saved plot with id {i} to {p}".format(p=path, i=plot_id))
    thumbnail = plot_name.replace(".png", "_thumb.png")

    fig.savefig(os.path.join(output_dir, thumbnail), dpi=20)
    plt.close(fig)
    log.debug("Saved plot to {p}".format(p=thumbnail))
    plot = Plot(plot_id, os.path.basename(plot_name),
                thumbnail=os.path.basename(thumbnail))

    return plot

create_readlength_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_READLENGTH,
    ("Read Length", "Reads", "Reads > Read Length"),
    80, "fulllength_nonchimeric_readlength_hist.png", get_blue(3))


def make_report(contig_set, summary_txt, output_dir):
    """
    Generate a report with ID, tables, attributes and plot groups.

    :param contig_set: an input FASTA file which has all full-length,
    non-chimeric reads produced by pbtranscript.py classify.

    This file is required to plot a read length histogram as part of
    the report:
         fulllength_nonchimeric_readlength_hist.png

    :param summary_txt: a summary TXT file with classify attributes,
    including 6 attributes,
Exemple #14
0
    thumbnail = plot_name.replace(".png", "_thumb.png")

    fig.savefig(os.path.join(output_dir, thumbnail), dpi=20)
    plt.close(fig)
    log.debug("Saved plot to {p}".format(p=thumbnail))
    plot = Plot(plot_id,
                os.path.basename(plot_name),
                thumbnail=os.path.basename(thumbnail))

    return plot


create_readlength_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_READLENGTH,
    ("Read Length", "Reads", "Reads > Read Length"), 80,
    "consensus_isoforms_readlength_hist.png", get_blue(3))

create_avgqv_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_AVGQV,
    ("HQ LQ Isoform Average QV", "Isoforms", "Isoforms > Average QV"), 80,
    "hq_lq_isoforms_avgqv_hist.png", get_blue(3))


def makeReport(inReadsFN, hq_isoforms_fq, lq_isoforms_fq, inSummaryFN, outDir):
    """
    Generate a report with ID, tables, attributes and plot groups.

    inReadsFN --- an input FASTA file which has all consensus
    isoforms produced by pbtranscript.py cluster.
    This file is required to plot a read length histogram as part of
    the report:
Exemple #15
0
# These functions create signatures (data, axis_labels, nbins, barcolor
_custom_read_length_histogram = functools.partial(_custom_histogram_with_cdf, "Mb > Read Length", 1000000)
_custom_read_accuracy_histogram = functools.partial(_custom_histogram_with_cdf, "Mb > Read Score", 1000000)


# These functions need to generate a function with signature (data,
# output_dir, dpi=)
create_readlength_plot = functools.partial(
    create_plot,
    _custom_read_length_histogram,
    Constants.P_READLENGTH,
    (get_plot_xlabel(spec, Constants.PG_READLENGTH, Constants.P_READLENGTH), "Reads", "bp > Read Length"),
    80,
    Constants.I_CCS_READ_LENGTH_HIST,
    get_blue(3),
)

create_accuracy_plot = functools.partial(
    create_plot,
    _custom_read_accuracy_histogram,
    Constants.P_ACCURACY,
    (get_plot_xlabel(spec, Constants.PG_ACCURACY, Constants.P_ACCURACY), "Reads", "bp > Read Score"),
    80,
    Constants.I_CCS_READ_ACCURACY_HIST,
    get_green(3),
)

create_npasses_plot = functools.partial(
    create_plot,
    _make_histogram,
Exemple #16
0
# These functions create signatures (data, axis_labels, nbins, barcolor)
_custom_read_length_histogram = functools.partial(_custom_histogram_with_cdf,
                                                  "Mb > Read Length", 1000000)
# FIXME the fallback label is incorrect!
_custom_read_accuracy_histogram = functools.partial(_custom_histogram_with_cdf,
                                                    "Mb > Read Score",
                                                    sys.maxint)

# These functions need to generate a function with signature (data,
# output_dir, dpi=)
create_readlength_plot = functools.partial(
    create_plot, _custom_read_length_histogram, Constants.P_READLENGTH,
    (get_plot_xlabel(spec, Constants.PG_READLENGTH,
                     Constants.P_READLENGTH), "Reads", "bp > Read Length"), 50,
    Constants.I_CCS_READ_LENGTH_HIST, get_blue(3))

create_accuracy_plot = functools.partial(
    create_plot, _custom_read_accuracy_histogram, Constants.P_ACCURACY,
    (get_plot_xlabel(spec, Constants.PG_ACCURACY,
                     Constants.P_ACCURACY), "Reads", "reads > Read Score"),
    100, Constants.I_CCS_READ_ACCURACY_HIST, get_green(3))

create_npasses_plot = functools.partial(
    create_plot, make_histogram, Constants.P_NPASSES,
    (get_plot_xlabel(spec, Constants.PG_NPASSES, Constants.P_NPASSES),
     get_plot_ylabel(spec, Constants.PG_NPASSES, Constants.P_NPASSES)), 80,
    Constants.I_CCS_NUM_PASSES_HIST, "#F18B17")

create_scatter_plot = functools.partial(
    create_plot, scatter_plot_accuracy_vs_numpasses, Constants.P_SCATTER,
    # PlotGroup
    PG_READLENGTH = "fulllength_nonchimeric_readlength_group"

    # Plots
    P_READLENGTH = "fulllength_nonchimeric_readlength_hist"

    # Table
    T_ATTR = "isoseq_classify_table"


spec = load_spec(Constants.R_ID)

create_readlength_plot = functools.partial(
    create_plot_impl, make_histogram_with_cdf, Constants.P_READLENGTH,
    ("Read Length", "Reads", "Reads > Read Length"), 80,
    "fulllength_nonchimeric_readlength_hist.png", get_blue(3))


def make_report(contig_set, summary_txt, output_dir):
    """
    Generate a report with ID, tables, attributes and plot groups.

    :param contig_set: an input FASTA file which has all full-length,
    non-chimeric reads produced by pbtranscript.py classify.

    This file is required to plot a read length histogram as part of
    the report:
         fulllength_nonchimeric_readlength_hist.png

    :param summary_txt: a summary TXT file with classify attributes,
    including 6 attributes,
Exemple #18
0
    return plot

# These functions create signatures (data, axis_labels, nbins, barcolor
_custom_read_length_histogram = functools.partial(
    _custom_histogram_with_cdf, "Mb > Read Length", 1000000)
_custom_read_accuracy_histogram = functools.partial(
    _custom_histogram_with_cdf, "Mb > Read Score", 1000000)


# These functions need to generate a function with signature (data,
# output_dir, dpi=)
create_readlength_plot = functools.partial(
    create_plot, _custom_read_length_histogram, Constants.P_READLENGTH,
    (get_plot_xlabel(spec, Constants.PG_READLENGTH, Constants.P_READLENGTH),
     "Reads", "bp > Read Length"),
    80, Constants.I_CCS_READ_LENGTH_HIST, get_blue(3))

create_accuracy_plot = functools.partial(
    create_plot, _custom_read_accuracy_histogram, Constants.P_ACCURACY,
    (get_plot_xlabel(spec, Constants.PG_ACCURACY, Constants.P_ACCURACY),
     "Reads", "bp > Read Score"),
    80, Constants.I_CCS_READ_ACCURACY_HIST, get_green(3))

create_npasses_plot = functools.partial(
    create_plot, _make_histogram, Constants.P_NPASSES,
    (get_plot_xlabel(spec, Constants.PG_NPASSES, Constants.P_NPASSES),
     get_plot_ylabel(spec, Constants.PG_NPASSES, Constants.P_NPASSES)),
    80, Constants.I_CCS_NUM_PASSES_HIST, "#F18B17")

create_scatter_plot = functools.partial(
    create_plot, scatter_plot_accuracy_vs_numpasses, Constants.P_SCATTER,
Exemple #19
0
    fig.savefig(os.path.join(output_dir, thumbnail), dpi=20)
    plt.close(fig)
    log.debug("Saved plot to {p}".format(p=thumbnail))
    plot = Plot(plot_id, os.path.basename(plot_name),
                thumbnail=os.path.basename(thumbnail))

    return plot

create_readlength_plot = functools.partial(
    __create_plot, _make_histogram_with_cdf, Constants.P_READLENGTH,
    (meta_rpt.get_meta_plotgroup(Constants.PG_READLENGTH).get_meta_plot(Constants.P_READLENGTH).xlabel,
     meta_rpt.get_meta_plotgroup(Constants.PG_READLENGTH).get_meta_plot(Constants.P_READLENGTH).ylabel["L"],
     meta_rpt.get_meta_plotgroup(Constants.PG_READLENGTH).get_meta_plot(Constants.P_READLENGTH).ylabel["R"]), 
     80,
     "consensus_isoforms_readlength_hist.png", get_blue(3))


def makeReport(inReadsFN, inSummaryFN, outDir):
    """
    Generate a report with ID, tables, attributes and plot groups.

    inReadsFN --- an input FASTA file which has all consensus
    isoforms produced by pbtranscript.py cluster.
    This file is required to plot a read length histogram as part of
    the report:
         consensus_isoforms_readlength_hist.png

    inSummaryFN --- a summary TXT file with cluster attributes,
    including two attributes:
         number of consensus isoforms