How to use the jcvi.graphics.base.plt.figure function in jcvi

def resample(args):
    """
    %prog resample yellow-catfish-resample.txt medicago-resample.txt

    Plot ALLMAPS performance across resampled real data.
    """
    p = OptionParser(resample.__doc__)
    opts, args, iopts = p.set_image_options(args, figsize="8x4", dpi=300)

    if len(args) != 2:
        sys.exit(not p.print_help())

    dataA, dataB = args
    fig = plt.figure(1, (iopts.w, iopts.h))
    root = fig.add_axes([0, 0, 1, 1])
    A = fig.add_axes([.1, .18, .32, .64])
    B = fig.add_axes([.6, .18, .32, .64])
    dataA = import_data(dataA)
    dataB = import_data(dataB)
    xlabel = "Fraction of markers"
    ylabels = ("Anchor rate", "Runtime (m)")
    legend = ("anchor rate", "runtime")
    subplot_twinx(A, dataA, xlabel, ylabels,
                     title="Yellow catfish", legend=legend)
    subplot_twinx(B, dataB, xlabel, ylabels,
                     title="Medicago", legend=legend)

    labels = ((.04, .92, "A"), (.54, .92, "B"))
    panel_labels(root, labels)

help="Do not plot chromosome circles",
    )
    p.add_option(
        "--shadestyle",
        default="curve",
        choices=Shade.Styles,
        help="Style of syntenic wedges",
    )
    opts, args, iopts = p.set_image_options(figsize="8x7")

    if len(args) != 2:
        sys.exit(not p.print_help())

    seqidsfile, layoutfile = args

    fig = plt.figure(1, (iopts.w, iopts.h))
    root = fig.add_axes([0, 0, 1, 1])

    Karyotype(
        fig,
        root,
        seqidsfile,
        layoutfile,
        plot_circles=(not opts.nocircles),
        shadestyle=opts.shadestyle,
        generank=(not opts.basepair),
    )

    root.set_xlim(0, 1)
    root.set_ylim(0, 1)
    root.set_axis_off()

def demo(args):
    """
    %prog demo

    Draw sample gene features to illustrate the various fates of duplicate
    genes - to be used in a book chapter.
    """
    p = OptionParser(demo.__doc__)
    opts, args = p.parse_args(args)

    fig = plt.figure(1, (8, 5))
    root = fig.add_axes([0, 0, 1, 1])

    panel_space = .23
    dup_space = .025
    # Draw a gene and two regulatory elements at these arbitrary locations
    locs = [(.5, .9), # ancestral gene
            (.5, .9 - panel_space + dup_space), # identical copies
            (.5, .9 - panel_space - dup_space),
            (.5, .9 - 2 * panel_space + dup_space), # degenerate copies
            (.5, .9 - 2 * panel_space - dup_space),
            (.2, .9 - 3 * panel_space + dup_space), # sub-functionalization
            (.2, .9 - 3 * panel_space - dup_space),
            (.5, .9 - 3 * panel_space + dup_space), # neo-functionalization
            (.5, .9 - 3 * panel_space - dup_space),
            (.8, .9 - 3 * panel_space + dup_space), # non-functionalization
            (.8, .9 - 3 * panel_space - dup_space),

if update_covfile:
            fw.write(row)
        data.append((tigID, rho, covStat, arrDist))

    print(msg.format(tigID), file=sys.stderr)

    from jcvi.graphics.base import plt, savefig

    logging.debug("Plotting {0} data points.".format(len(data)))
    tigID, rho, covStat, arrDist = zip(*data)

    y = arrDist if plot_arrDist else covStat
    ytag = "arrDist" if plot_arrDist else "covStat"

    fig = plt.figure(1, (7, 7))
    ax = fig.add_axes([.12, .1, .8, .8])
    ax.plot(rho, y, ".", color="lightslategrey")

    xtag = "rho"
    info = (genome, xtag, ytag)
    title = "{0} {1} vs. {2}".format(*info)
    ax.set_title(title)
    ax.set_xlabel(xtag)
    ax.set_ylabel(ytag)

    if plot_arrDist:
        ax.set_yscale('log')

    imagename = "{0}.png".format(".".join(info))
    savefig(imagename, dpi=150)

def lms(args):
    """
    %prog lms

    ALLMAPS cartoon to illustrate LMS metric.
    """
    from random import randint
    from jcvi.graphics.chromosome import HorizontalChromosome

    p = OptionParser(lms.__doc__)
    opts, args, iopts = p.set_image_options(args, figsize="6x6", dpi=300)

    fig = plt.figure(1, (iopts.w, iopts.h))
    root = fig.add_axes([0, 0, 1, 1])

    # Panel A
    w, h = .7, .35
    ax = fig.add_axes([.15, .6, w, h])

    xdata = [x + randint(-3, 3) for x in range(10, 110, 10)]
    ydata = [x + randint(-3, 3) for x in range(10, 110, 10)]
    ydata[3:7] = ydata[3:7][::-1]
    xydata = zip(xdata, ydata)
    lis = xydata[:3] + [xydata[4]] + xydata[7:]
    lds = xydata[3:7]
    xlis, ylis = zip(*lis)
    xlds, ylds = zip(*lds)
    ax.plot(xlis, ylis, "r-", lw=12, alpha=.3,
                              solid_capstyle="round", solid_joinstyle="round")

format(st.median, st.firstq, st.thirdq)
        title += "Mean:{0:.3f}|Std:{1:.3f}||N:{2})".\
                format(st.mean, st.sd, st.size)

        tbins = (0, ks_max, bins) if ks else (0, .6, 10)
        digit = 2 if (ks_max * 1. / bins) < .1 else 1
        stem_leaf_plot(columndata, *tbins, digit=digit, title=title)

    if not opts.pdf:
        return

    components = opts.components
    data = [x.ng_ks for x in data]
    data = [x for x in data if ks_min <= x <= ks_max]

    fig = plt.figure(1, (iopts.w, iopts.h))
    ax = fig.add_axes([.12, .1, .8, .8])
    kp = KsPlot(ax, ks_max, opts.bins, legendp=opts.legendp)
    kp.add_data(data, components, fill=opts.fill, fitted=opts.fit)
    kp.draw(title=opts.title)

assert seqid in allseqids, "{0} not in {1}".format(seqid, allseqids)

    s = Scaffold(seqid, cc)
    mlgs = [k for k, v in s.mlg_counts.items() if v >= links]
    while not mlgs:
        links /= 2
        logging.error("No markers to plot, --links reset to {0}".format(links))
        mlgs = [k for k, v in s.mlg_counts.items() if v >= links]

    mlgsizes = {}
    for mlg in mlgs:
        mm = cc.extract_mlg(mlg)
        mlgsize = max(function(x) for x in mm)
        mlgsizes[mlg] = mlgsize

    fig = plt.figure(1, (iopts.w, iopts.h))
    root = fig.add_axes([0, 0, 1, 1])
    bbox = dict(boxstyle="round", fc='darkslategray', ec='darkslategray')
    if opts.title:
        root.text(.5, .95, opts.title, color="w", bbox=bbox, size=16)
    ax1 = fig.add_axes([0, 0, .5, 1])
    ax2 = fig.add_axes([.5, 0, .5, 1])

    # Find the layout first
    ystart, ystop = .9, .1
    L = Layout(mlgsizes)
    coords = L.coords

    tip = .02
    marker_pos = {}
    # Palette
    colors = dict((mapname, set2[i % len(set2)]) for i, mapname in enumerate(mapnames))