Ejemplo n.º 1
0
def draw_gene_legend(
    ax,
    x1,
    x2,
    ytop,
    d=0.04,
    text=False,
    repeat=False,
    glyphstyle="box",
):
    forward, backward = OrientationPalette.forward, OrientationPalette.backward
    ax.plot([x1, x1 + d], [ytop, ytop], ":", color=forward, lw=2)
    ax.plot([x1 + d], [ytop], ">", color=forward, mec=forward)
    ax.plot([x2, x2 + d], [ytop, ytop], ":", color=backward, lw=2)
    ax.plot([x2], [ytop], "<", color=backward, mec="g")
    if text:
        ax.text(x1 + d / 2, ytop + d / 2, "gene (+)", ha="center")
        ax.text(x2 + d / 2, ytop + d / 2, "gene (-)", ha="center")
    if repeat:
        xr = (x1 + x2 + d) / 2
        Glyph(
            ax,
            xr - d / 2,
            xr + d / 2,
            ytop,
            0.012 * 3 / 4,
            gradient=False,
            fc="#ff7f00",
            style=glyphstyle,
            zorder=2,
        )
        ax.text(xr, ytop + d / 2, "repeat", ha="center")
Ejemplo n.º 2
0
def draw_gene_legend(ax, x1, x2, ytop, d=.04, text=False, repeat=False):
    ax.plot([x1, x1 + d], [ytop, ytop], ":", color=forward, lw=2)
    ax.plot([x1 + d], [ytop], ">", color=forward, mec=forward)
    ax.plot([x2, x2 + d], [ytop, ytop], ":", color=backward, lw=2)
    ax.plot([x2], [ytop], "<", color=backward, mec="g")
    if text:
        ax.text(x1 + d / 2, ytop + d / 2, "gene (+)", ha="center")
        ax.text(x2 + d / 2, ytop + d / 2, "gene (-)", ha="center")
    if repeat:
        xr = (x1 + x2 + d) / 2
        Glyph(ax, xr - d / 2, xr + d / 2, ytop, .012 * 3 / 4, gradient=False,
              fc='#ff7f00', zorder=2)
        ax.text(xr, ytop + d / 2, "repeat", ha="center")
Ejemplo n.º 3
0
    def __init__(self, ax, ext, layout, bed, scale, switch=None,
                 chr_label=True, loc_label=True,
                 pad=.05, vpad=.015, extra_features=None):
        x, y = layout.x, layout.y
        ratio = layout.ratio
        scale /= ratio
        self.y = y
        lr = layout.rotation
        tr = mpl.transforms.Affine2D().\
                    rotate_deg_around(x, y, lr) + ax.transAxes
        inv = ax.transAxes.inverted()

        start, end, si, ei, chr, orientation, span = ext
        flank = span / scale / 2
        xstart, xend = x - flank, x + flank
        self.xstart, self.xend = xstart, xend

        cv = lambda t: xstart + abs(t - startbp) / scale
        hidden = layout.hidden

        # Chromosome
        if not hidden:
            ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
                    lw=2, zorder=1)

        self.genes = genes = bed[si: ei + 1]
        startbp, endbp = start.start, end.end
        if orientation == '-':
            startbp, endbp = endbp, startbp

        if switch:
            chr = switch.get(chr, chr)
        if layout.label:
            chr = layout.label

        label = "-".join((human_size(startbp, target="Mb", precision=2)[:-2],
                          human_size(endbp, target="Mb", precision=2)))

        height = .012
        self.gg = {}
        # Genes
        for g in genes:
            gstart, gend = g.start, g.end
            strand = g.strand
            if strand == '-':
                gstart, gend = gend, gstart
            if orientation == '-':
                strand = "+" if strand == "-" else "-"

            x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
            self.gg[g.accn] = (a, b)

            color = forward if strand == "+" else backward
            if not hidden:
                gp = Glyph(ax, x1, x2, y, height, gradient=False, fc=color, zorder=3)
                gp.set_transform(tr)

        # Extra features (like repeats)
        if extra_features:
            for g in extra_features:
                gstart, gend = g.start, g.end
                x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
                gp = Glyph(ax, x1, x2, y, height * 3 / 4, gradient=False,
                           fc='#ff7f00', zorder=2)
                gp.set_transform(tr)

        ha, va = layout.ha, layout.va

        hpad = .02
        if ha == "left":
            xx = xstart - hpad
            ha = "right"
        elif ha == "right":
            xx = xend + hpad
            ha = "left"
        else:
            xx = x
            ha = "center"

        # Tentative solution to labels stick into glyph
        magic = 40.
        cc = abs(lr) / magic if abs(lr) > magic else 1
        if va == "top":
            yy = y + cc * pad
        elif va == "bottom":
            yy = y - cc * pad
        else:
            yy = y

        l = np.array((xx, yy))
        trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
                                                    l.reshape((1, 2)))[0]
        lx, ly = l
        if not hidden:
            bbox = dict(boxstyle="round", fc='w', ec='w', alpha=.5)
            kwargs = dict(ha=ha, va="center",
                          rotation=trans_angle, bbox=bbox, zorder=10)

            # TODO: I spent several hours on trying to make this work - with no
            # good solutions. To generate labels on multiple lines, each line
            # with a different style is difficult in matplotlib. The only way,
            # if you can tolerate an extra dot (.), is to use the recipe below.
            #chr_label = r"\noindent " + markup(chr) + r" \\ ." if chr_label else None
            #loc_label = r"\noindent . \\ " + label if loc_label else None

            chr_label = markup(chr) if chr_label else None
            loc_label = label if loc_label else None
            if chr_label:
                if loc_label:
                    ax.text(lx, ly + vpad, chr_label, color=layout.color, **kwargs)
                    ax.text(lx, ly - vpad, loc_label, color="lightslategrey",
                            size=10, **kwargs)
                else:
                    ax.text(lx, ly, chr_label, color=layout.color, **kwargs)
Ejemplo n.º 4
0
    def __init__(
        self,
        ax,
        ext,
        layout,
        bed,
        scale,
        switch=None,
        chr_label=True,
        loc_label=True,
        genelabelsize=0,
        pad=0.05,
        vpad=0.015,
        extra_features=None,
        glyphstyle="box",
        glyphcolor: BasePalette = OrientationPalette(),
    ):
        x, y = layout.x, layout.y
        ratio = layout.ratio
        scale /= ratio
        self.y = y
        lr = layout.rotation
        tr = mpl.transforms.Affine2D().rotate_deg_around(x, y, lr) + ax.transAxes
        inv = ax.transAxes.inverted()

        start, end, si, ei, chr, orientation, span = ext
        flank = span / scale / 2
        xstart, xend = x - flank, x + flank
        self.xstart, self.xend = xstart, xend

        cv = lambda t: xstart + abs(t - startbp) / scale
        hidden = layout.hidden

        # Chromosome
        if not hidden:
            ax.plot((xstart, xend), (y, y), color="gray", transform=tr, lw=2, zorder=1)

        self.genes = genes = bed[si : ei + 1]
        startbp, endbp = start.start, end.end
        if orientation == "-":
            startbp, endbp = endbp, startbp

        if switch:
            chr = switch.get(chr, chr)
        if layout.label:
            chr = layout.label

        label = "-".join(
            (
                human_size(startbp, target="Mb", precision=2)[:-2],
                human_size(endbp, target="Mb", precision=2),
            )
        )

        height = 0.012
        self.gg = {}
        # Genes
        for g in genes:
            gstart, gend = g.start, g.end
            strand = g.strand
            if strand == "-":
                gstart, gend = gend, gstart
            if orientation == "-":
                strand = "+" if strand == "-" else "-"

            x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
            gene_name = g.accn
            self.gg[gene_name] = (a, b)

            color, zorder = (
                glyphcolor.get_color_and_zorder(strand)
                if isinstance(glyphcolor, OrientationPalette)
                else glyphcolor.get_color_and_zorder(gene_name)
            )

            if hidden:
                continue
            gp = Glyph(
                ax,
                x1,
                x2,
                y,
                height,
                gradient=False,
                fc=color,
                style=glyphstyle,
                zorder=zorder,
            )
            gp.set_transform(tr)
            if genelabelsize:
                ax.text(
                    (x1 + x2) / 2,
                    y + height / 2 + genelabelsize * vpad / 3,
                    markup(gene_name),
                    size=genelabelsize,
                    rotation=25,
                    ha="left",
                    va="center",
                    color="lightslategray",
                )

        # Extra features (like repeats)
        if extra_features:
            for g in extra_features:
                gstart, gend = g.start, g.end
                x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
                gp = Glyph(
                    ax,
                    x1,
                    x2,
                    y,
                    height * 3 / 4,
                    gradient=False,
                    fc="#ff7f00",
                    style=glyphstyle,
                    zorder=2,
                )
                gp.set_transform(tr)

        ha, va = layout.ha, layout.va

        hpad = 0.02
        if ha == "left":
            xx = xstart - hpad
            ha = "right"
        elif ha == "right":
            xx = xend + hpad
            ha = "left"
        else:
            xx = x
            ha = "center"

        # Tentative solution to labels stick into glyph
        magic = 40.0
        cc = abs(lr) / magic if abs(lr) > magic else 1
        if va == "top":
            yy = y + cc * pad
        elif va == "bottom":
            yy = y - cc * pad
        else:
            yy = y

        l = np.array((xx, yy))
        trans_angle = ax.transAxes.transform_angles(np.array((lr,)), l.reshape((1, 2)))[
            0
        ]
        lx, ly = l
        if not hidden:
            bbox = dict(boxstyle="round", fc="w", ec="w", alpha=0.5)
            kwargs = dict(
                ha=ha, va="center", rotation=trans_angle, bbox=bbox, zorder=10
            )

            # TODO: I spent several hours on trying to make this work - with no
            # good solutions. To generate labels on multiple lines, each line
            # with a different style is difficult in matplotlib. The only way,
            # if you can tolerate an extra dot (.), is to use the recipe below.
            # chr_label = r"\noindent " + markup(chr) + r" \\ ." if chr_label else None
            # loc_label = r"\noindent . \\ " + label if loc_label else None

            chr_label = markup(chr) if chr_label else None
            loc_label = label if loc_label else None
            if chr_label:
                if loc_label:
                    ax.text(lx, ly + vpad, chr_label, color=layout.color, **kwargs)
                    ax.text(
                        lx,
                        ly - vpad,
                        loc_label,
                        color="lightslategrey",
                        size=10,
                        **kwargs
                    )
                else:
                    ax.text(lx, ly, chr_label, color=layout.color, **kwargs)
Ejemplo n.º 5
0
    def __init__(self, ax, ext, layout, bed, scale, switch=None,
                 chr_label=True, pad=.04, vpad=.012, extra_features=None):
        x, y = layout.x, layout.y
        ratio = layout.ratio
        scale /= ratio
        self.y = y
        lr = layout.rotation
        tr = mpl.transforms.Affine2D().\
                    rotate_deg_around(x, y, lr) + ax.transAxes
        inv = ax.transAxes.inverted()

        start, end, si, ei, chr, orientation, span = ext
        flank = span / scale / 2
        xstart, xend = x - flank, x + flank
        self.xstart, self.xend = xstart, xend

        cv = lambda t: xstart + abs(t - startbp) / scale
        hidden = layout.hidden

        # Chromosome
        if not hidden:
            ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
                    lw=2, zorder=1)

        self.genes = genes = bed[si: ei + 1]
        startbp, endbp = start.start, end.end
        if orientation == '-':
            startbp, endbp = endbp, startbp

        if switch:
            chr = switch.get(chr, chr)
        label = "-".join((human_size(startbp, target="Mb")[:-2],
                          human_size(endbp, target="Mb")))

        height = .012
        self.gg = {}
        # Genes
        for g in genes:
            gstart, gend = g.start, g.end
            strand = g.strand
            if strand == '-':
                gstart, gend = gend, gstart
            if orientation == '-':
                strand = "+" if strand == "-" else "-"

            x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
            self.gg[g.accn] = (a, b)

            color = forward if strand == "+" else backward
            if not hidden:
                gp = Glyph(ax, x1, x2, y, height, gradient=False, fc=color, zorder=3)
                gp.set_transform(tr)

        # Extra features (like repeats)
        if extra_features:
            for g in extra_features:
                gstart, gend = g.start, g.end
                x1, x2, a, b = self.get_coordinates(gstart, gend, y, cv, tr, inv)
                gp = Glyph(ax, x1, x2, y, height * 3 / 4, gradient=False,
                           fc='#ff7f00', zorder=2)
                gp.set_transform(tr)

        ha, va = layout.ha, layout.va

        hpad = .02
        if ha == "left":
            xx = xstart - hpad
            ha = "right"
        elif ha == "right":
            xx = xend + hpad
            ha = "left"
        else:
            xx = x
            ha = "center"

        # Tentative solution to labels stick into glyph
        magic = 40.
        cc = abs(lr) / magic if abs(lr) > magic else 1
        if va == "top":
            yy = y + cc * pad
        elif va == "bottom":
            yy = y - cc * pad - .01
        else:
            yy = y

        l = np.array((xx, yy))
        trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
                                                    l.reshape((1, 2)))[0]
        lx, ly = l
        if not hidden and chr_label:
            bbox = dict(boxstyle="round", fc='w', ec='w', alpha=.5)
            ax.text(lx, ly + vpad, markup(chr), color=layout.color,
                        ha=ha, va="center", rotation=trans_angle,
                        bbox=bbox, zorder=10)
            ax.text(lx, ly - vpad, label, color="lightslategrey", size=10,
                        ha=ha, va="center", rotation=trans_angle,
                        bbox=bbox, zorder=10)
Ejemplo n.º 6
0
    def __init__(self, ax, ext, layout, bed, scale, switch=None, chr_label=True,
                 pad=.04, vpad=.012):
        x, y = layout.x, layout.y
        ratio = layout.ratio
        scale /= ratio
        self.y = y
        lr = layout.rotation
        tr = Affine2D().rotate_deg_around(x, y, lr) + ax.transAxes
        inv = ax.transAxes.inverted()

        start, end, si, ei, chr, orientation, span = ext
        flank = span / scale / 2
        xstart, xend = x - flank, x + flank
        self.xstart, self.xend = xstart, xend

        cv = lambda t: xstart + abs(t - startbp) / scale
        hidden = layout.hidden

        # Chromosome
        if not hidden:
            ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
                    lw=2, zorder=1)

        self.genes = genes = bed[si: ei + 1]
        startbp, endbp = start.start, end.end
        if orientation == '-':
            startbp, endbp = endbp, startbp

        if switch:
            chr = switch.get(chr, chr)
        label = "-".join((human_size(startbp, target="Mb")[:-2],
                          human_size(endbp, target="Mb")))

        height = .012
        self.gg = {}
        # Genes
        for g in genes:
            gstart, gend = g.start, g.end
            strand = g.strand
            if strand == '-':
                gstart, gend = gend, gstart
            if orientation == '-':
                strand = "+" if strand == "-" else "-"

            x1, x2 = cv(gstart), cv(gend)
            a, b = tr.transform((x1, y)), tr.transform((x2, y))
            a, b = inv.transform(a), inv.transform(b)
            self.gg[g.accn] = (a, b)

            color = "b" if strand == "+" else "g"
            if not hidden:
                gp = Glyph(ax, x1, x2, y, height, gradient=False, fc=color, zorder=3)
                gp.set_transform(tr)

        ha, va = layout.ha, layout.va

        hpad = .02
        if ha == "left":
            xx = xstart - hpad
            ha = "right"
        elif ha == "right":
            xx = xend + hpad
            ha = "left"
        else:
            xx = x
            ha = "center"

        # Tentative solution to labels stick into glyph
        magic = 40.
        cc = abs(lr) / magic if abs(lr) > magic else 1
        if va == "top":
            yy = y + cc * pad
        elif va == "bottom":
            yy = y - cc * pad
        else:
            yy = y

        l = np.array((xx, yy))
        trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
                                                    l.reshape((1, 2)))[0]
        lx, ly = l
        if not hidden and chr_label:
            ax.text(lx, ly + vpad, markup(chr), color=layout.color,
                        ha=ha, va="center", rotation=trans_angle)
            ax.text(lx, ly - vpad, label, color="k",
                        ha=ha, va="center", rotation=trans_angle)
Ejemplo n.º 7
0
    def __init__(self,
                 ax,
                 ext,
                 layout,
                 bed,
                 scale,
                 switch=None,
                 chr_label=True,
                 pad=.04,
                 vpad=.012):
        x, y = layout.x, layout.y
        ratio = layout.ratio
        scale /= ratio
        self.y = y
        lr = layout.rotation
        tr = mpl.transforms.Affine2D().\
                    rotate_deg_around(x, y, lr) + ax.transAxes
        inv = ax.transAxes.inverted()

        start, end, si, ei, chr, orientation, span = ext
        flank = span / scale / 2
        xstart, xend = x - flank, x + flank
        self.xstart, self.xend = xstart, xend

        cv = lambda t: xstart + abs(t - startbp) / scale
        hidden = layout.hidden

        # Chromosome
        if not hidden:
            ax.plot((xstart, xend), (y, y), color="gray", transform=tr, \
                    lw=2, zorder=1)

        self.genes = genes = bed[si:ei + 1]
        startbp, endbp = start.start, end.end
        if orientation == '-':
            startbp, endbp = endbp, startbp

        if switch:
            chr = switch.get(chr, chr)
        label = "-".join(
            (human_size(startbp,
                        target="Mb")[:-2], human_size(endbp, target="Mb")))

        height = .012
        self.gg = {}
        # Genes
        for g in genes:
            gstart, gend = g.start, g.end
            strand = g.strand
            if strand == '-':
                gstart, gend = gend, gstart
            if orientation == '-':
                strand = "+" if strand == "-" else "-"

            x1, x2 = cv(gstart), cv(gend)
            a, b = tr.transform((x1, y)), tr.transform((x2, y))
            a, b = inv.transform(a), inv.transform(b)
            self.gg[g.accn] = (a, b)

            color = "b" if strand == "+" else "g"
            if not hidden:
                gp = Glyph(ax,
                           x1,
                           x2,
                           y,
                           height,
                           gradient=False,
                           fc=color,
                           zorder=3)
                gp.set_transform(tr)

        ha, va = layout.ha, layout.va

        hpad = .02
        if ha == "left":
            xx = xstart - hpad
            ha = "right"
        elif ha == "right":
            xx = xend + hpad
            ha = "left"
        else:
            xx = x
            ha = "center"

        # Tentative solution to labels stick into glyph
        magic = 40.
        cc = abs(lr) / magic if abs(lr) > magic else 1
        if va == "top":
            yy = y + cc * pad
        elif va == "bottom":
            yy = y - cc * pad
        else:
            yy = y

        l = np.array((xx, yy))
        trans_angle = ax.transAxes.transform_angles(np.array((lr, )),
                                                    l.reshape((1, 2)))[0]
        lx, ly = l
        if not hidden and chr_label:
            ax.text(lx,
                    ly + vpad,
                    markup(chr),
                    color=layout.color,
                    ha=ha,
                    va="center",
                    rotation=trans_angle)
            ax.text(lx,
                    ly - vpad,
                    label,
                    color="k",
                    ha=ha,
                    va="center",
                    rotation=trans_angle)