Exemplo n.º 1
0
    def draw(self, roundrect=False, plot_label=True):
        if self.empty:
            return

        y = self.y
        color = self.color
        ax = self.ax
        xstart = self.xstart
        gap = self.gap
        va = self.va
        nseqids = len(self.seqids)
        tr = self.tr
        for i, sid in enumerate(self.seqids):
            size = self.sizes[sid]
            rsize = self.ratio * size
            xend = xstart + rsize
            hc = HorizontalChromosome(ax,
                                      xstart,
                                      xend,
                                      y,
                                      height=self.height,
                                      lw=self.lw,
                                      fc=color,
                                      roundrect=roundrect)
            hc.set_transform(tr)
            sid = sid.rsplit("_", 1)[-1]
            si = "".join(x for x in sid if x not in string.letters)
            si = str(int(si))
            xx = (xstart + xend) / 2
            xstart = xend + gap

            if nseqids > 2 * MaxSeqids and (i + 1) % 10 != 0:
                continue
            if nseqids < 5:
                continue

            pad = .02
            if va == "bottom":
                pad = -pad
            TextCircle(ax,
                       xx,
                       y + pad,
                       si,
                       radius=.01,
                       fc="w",
                       color=color,
                       size=10,
                       transform=tr)

        xp = min(self.xstart / 2, .1) if (self.xstart + self.xend) / 2 <= .5 \
                                      else max(1 - self.end / 2, .92)
        label = markup(self.label)
        c = color if color != "gainsboro" else "k"
        if plot_label:
            ax.text(xp,
                    y + self.height * .6,
                    label,
                    ha="center",
                    color=c,
                    transform=tr)
Exemplo n.º 2
0
    def draw(self, roundrect=False, plot_label=True, plot_circles=True,
             pad=.03, vpad=.09):
        if self.empty:
            return

        y = self.y
        color = self.color
        ax = self.ax
        xstart = self.xstart
        gap = self.gap
        va = self.va
        nseqids = len(self.seqids)
        tr = self.tr

        def make_circle_name(sid):
            sid = sid.rsplit("_", 1)[-1]
            si = "".join(x for x in sid if x in string.digits)
            si = str(int(si))
            if sid in self.rev:
                si += '-'
            return si

        for i, sid in enumerate(self.seqids):
            size = self.sizes[sid]
            rsize = self.ratio * size
            xend = xstart + rsize
            hc = HorizontalChromosome(ax, xstart, xend, y,
                                      height=self.height, lw=self.lw, fc=color,
                                      roundrect=roundrect)
            hc.set_transform(tr)
            si = make_circle_name(sid)
            xx = (xstart + xend) / 2
            xstart = xend + gap

            step = 2 if nseqids <= 40 else 10
            if nseqids >= 2 * MaxSeqids and (i + 1) % step != 0:
                continue
            if nseqids < 5:
                continue

            hpad = -pad if va == "bottom" else pad
            if plot_circles:
                TextCircle(ax, xx, y + hpad, si, radius=.01,
                           fc="w", color=color, size=10, transform=tr)

        label = markup(self.label)
        c = color if color != "gainsboro" else "k"
        if plot_label:
            if self.label_va == "top":
                x, y = self.x, self.y + vpad
            elif self.label_va == "bottom":
                x, y = self.x, self.y - vpad
            else:  # "center"
                x, y = self.xstart - vpad, self.y
            ax.text(x, y, label, ha="center", va="center", color=c, transform=tr)
Exemplo n.º 3
0
    def draw(self, roundrect=False, plot_label=True):
        if self.empty:
            return

        y = self.y
        color = self.color
        ax = self.ax
        xstart = self.xstart
        gap = self.gap
        va = self.va
        nseqids = len(self.seqids)
        tr = self.tr
        for i, sid in enumerate(self.seqids):
            size = self.sizes[sid]
            rsize = self.ratio * size
            xend = xstart + rsize
            hc = HorizontalChromosome(ax, xstart, xend, y,
                                      height=self.height, lw=self.lw, fc=color,
                                      roundrect=roundrect)
            hc.set_transform(tr)
            sid = sid.rsplit("_", 1)[-1]
            si = "".join(x for x in sid if x not in string.letters)
            si = str(int(si))
            xx = (xstart + xend) / 2
            xstart = xend + gap

            if nseqids > 2 * MaxSeqids and (i + 1) % 10 != 0:
                continue
            if nseqids < 5:
                continue

            pad = .02
            if va == "bottom":
                pad = - pad
            TextCircle(ax, xx, y + pad, si, radius=.01,
                       fc="w", color=color, size=10, transform=tr)

        xp = min(self.xstart / 2, .1) if (self.xstart + self.xend) / 2 <= .5 \
                                      else max(1 - self.xend / 2, .92)
        label = markup(self.label)
        c = color if color != "gainsboro" else "k"
        if plot_label:
            ax.text(xp, y + self.height * .6, label,
                    ha="center", color=c, transform=tr)
Exemplo n.º 4
0
    def draw(self, roundrect=False, plot_label=True, pad=.03, vpad=.09):
        if self.empty:
            return

        y = self.y
        color = self.color
        ax = self.ax
        xstart = self.xstart
        gap = self.gap
        va = self.va
        nseqids = len(self.seqids)
        tr = self.tr
        for i, sid in enumerate(self.seqids):
            size = self.sizes[sid]
            rsize = self.ratio * size
            xend = xstart + rsize
            hc = HorizontalChromosome(ax,
                                      xstart,
                                      xend,
                                      y,
                                      height=self.height,
                                      lw=self.lw,
                                      fc=color,
                                      roundrect=roundrect)
            hc.set_transform(tr)
            sid = sid.rsplit("_", 1)[-1]
            si = "".join(x for x in sid if x in string.digits)
            si = str(int(si))
            xx = (xstart + xend) / 2
            xstart = xend + gap

            step = 2 if nseqids <= 40 else 10
            if nseqids >= 2 * MaxSeqids and (i + 1) % step != 0:
                continue
            if nseqids < 5:
                continue

            hpad = -pad if va == "bottom" else pad
            TextCircle(ax,
                       xx,
                       y + hpad,
                       si,
                       radius=.01,
                       fc="w",
                       color=color,
                       size=10,
                       transform=tr)

        label = markup(self.label)
        c = color if color != "gainsboro" else "k"
        if plot_label:
            if self.label_va == "top":
                x, y = self.x, self.y + vpad
                va = "bottom"
            elif self.label_va == "bottom":
                x, y = self.x, self.y - vpad
                va = "top"
            else:  # "center"
                x, y = self.xstart - vpad, self.y
                va = "center"
            ax.text(x,
                    y,
                    label,
                    ha="center",
                    va="center",
                    color=c,
                    transform=tr)
Exemplo n.º 5
0
    def draw(self,
             roundrect=False,
             plot_label=True,
             plot_circles=True,
             pad=0.03,
             vpad=0.09):
        if self.empty:
            return

        y = self.y
        color = self.color
        ax = self.ax
        xstart = self.xstart
        gap = self.gap
        va = self.va
        nseqids = len(self.seqids)
        tr = self.tr

        for i, sid in enumerate(self.seqids):
            size = self.sizes[sid]
            rsize = self.ratio * size
            xend = xstart + rsize
            hc = HorizontalChromosome(
                ax,
                xstart,
                xend,
                y,
                height=self.height,
                lw=self.lw,
                fc=color,
                roundrect=roundrect,
            )
            hc.set_transform(tr)
            si = make_circle_name(sid, self.rev)
            xx = (xstart + xend) / 2
            xstart = xend + gap

            step = 2 if nseqids <= 40 else 10
            if nseqids >= 2 * MaxSeqids and (i + 1) % step != 0:
                continue
            if nseqids < 5:
                continue

            hpad = -pad if va == "bottom" else pad
            if plot_circles:
                TextCircle(
                    ax,
                    xx,
                    y + hpad,
                    si,
                    fc="w",
                    color=color,
                    size=10,
                    transform=tr,
                )

        label = markup(self.label)
        c = color if color != "gainsboro" else "k"
        if plot_label:
            if self.label_va == "top":
                x, y = self.x, self.y + vpad
            elif self.label_va == "bottom":
                x, y = self.x, self.y - vpad
            else:  # "center"
                x, y = self.xstart - vpad / 2, self.y
            ax.text(x,
                    y,
                    label,
                    ha="center",
                    va="center",
                    color=c,
                    transform=tr)