コード例 #1
0
ファイル: ab_coding.py プロジェクト: fw1121/ngs_crumbs
 def plot_parent_coding_hist(self, fhand):
     fig = Figure()
     axes = fig.add_subplot(111)
     axes.hist(self.indexes, fill=True, log=True, bins=20, rwidth=1)
     axes.axvline(x=self.parent_index_threshold)
     axes.set_xlabel('support index for parental coding')
     axes.set_ylabel('num. SNPs')
     _print_figure(axes, fig, fhand, plot_legend=False)
コード例 #2
0
 def plot_parent_coding_hist(self, fhand):
     fig = Figure()
     axes = fig.add_subplot(111)
     axes.hist(self.indexes, fill=True, log=True, bins=20, rwidth=1)
     axes.axvline(x=self.parent_index_threshold)
     axes.set_xlabel('support index for parental coding')
     axes.set_ylabel('num. SNPs')
     _print_figure(axes, fig, fhand, plot_legend=False)
コード例 #3
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 def draw_hist(self, fhand):
     fig = Figure()
     axes = fig.add_subplot(111)
     axes.hist(self._scores, fill=True, log=True, bins=20,
               rwidth=1)
     axes.axvline(x=self.threshold)
     axes.set_xlabel('% complexity score')
     axes.set_ylabel('num. SNPs')
     _print_figure(axes, fig, fhand, plot_legend=False)
コード例 #4
0
ファイル: annotation.py プロジェクト: fw1121/ngs_crumbs
 def draw_hist(self, fhand):
     fig = Figure()
     axes = fig.add_subplot(111)
     axes.hist(self._scores, fill=True, log=True, bins=20,
               rwidth=1)
     axes.axvline(x=self.threshold)
     axes.set_xlabel('% complexity score')
     axes.set_ylabel('num. SNPs')
     _print_figure(axes, fig, fhand, plot_legend=False)
コード例 #5
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    def plot_smooth_hist(self, fhand):
        bins = 20
        fig = Figure()
        axes2 = fig.add_subplot(111)
        x = self._smoothes
        y = self._recombs
        image = axes2.hist2d(x, y, bins=bins, norm=LogNorm())[-1]

        axes2.tick_params(
            which='both',  # both major and minor ticks are affected
            bottom='off',  # ticks along the bottom edge are off
            top='off',  # ticks along the top edge are off
            labelbottom='off',
            right='off',
            left='off',
            labelleft='off')
        xmin2d, xmax2d = axes2.get_xlim()
        ymin2d, ymax2d = axes2.get_ylim()
        axes2.vlines(self.smooth_threhsold, ymin2d, ymax2d, color='r')
        if self.recomb_threshold is not None:
            axes2.hlines(self.recomb_threshold, xmin2d, xmax2d, color='r')

        divider = make_axes_locatable(axes2)
        cax = divider.append_axes("right", size="5%", pad=0.05)
        fig.colorbar(image, cax=cax)

        axes = divider.append_axes('bottom', size=2, pad=0.1, sharex=axes2)

        #axes = fig.add_subplot(224)
        #print axes2.get_position().bounds
        axes.hist(x, fill=True, log=True, bins=bins, rwidth=1)
        axes.set_xlabel('Smooth index')
        axes.set_ylabel('Num. SNPs')
        axes.set_xlim(xmin2d, xmax2d)
        ymin, ymax = axes.get_ylim()
        axes.vlines(self.smooth_threhsold, ymin, ymax, color='r')

        axes = divider.append_axes('left', size=2, pad=0.1, sharey=axes2)
        #axes = fig.add_subplot(221)
        axes.hist(y,
                  orientation='horizontal',
                  fill=True,
                  log=True,
                  bins=bins,
                  rwidth=1)
        axes.set_ylabel('Num. recombs.')
        axes.set_xlabel('Num. SNPs')
        _print_figure(axes, fig, fhand, plot_legend=False)
        axes.set_ylim(ymin2d, ymax2d)
        xmin, xmax = axes.get_xlim()
        if self.recomb_threshold is not None:
            axes.hlines(self.recomb_threshold, xmin, xmax, color='r')
コード例 #6
0
ファイル: ab_coding.py プロジェクト: fw1121/ngs_crumbs
    def plot_smooth_hist(self, fhand):
        bins = 20
        fig = Figure()
        axes2 = fig.add_subplot(111)
        x = self._smoothes
        y = self._recombs
        image = axes2.hist2d(x, y, bins=bins,
                             norm=LogNorm())[-1]

        axes2.tick_params(
        which='both',      # both major and minor ticks are affected
        bottom='off',      # ticks along the bottom edge are off
        top='off',         # ticks along the top edge are off
        labelbottom='off',
        right='off', left='off', labelleft='off')
        xmin2d, xmax2d = axes2.get_xlim()
        ymin2d, ymax2d = axes2.get_ylim()
        axes2.vlines(self.smooth_threhsold, ymin2d, ymax2d, color='r')
        if self.recomb_threshold is not None:
            axes2.hlines(self.recomb_threshold, xmin2d, xmax2d, color='r')

        divider = make_axes_locatable(axes2)
        cax = divider.append_axes("right", size="5%", pad=0.05)
        fig.colorbar(image, cax=cax)

        axes = divider.append_axes('bottom', size=2, pad=0.1, sharex=axes2)

        #axes = fig.add_subplot(224)
        #print axes2.get_position().bounds
        axes.hist(x, fill=True, log=True, bins=bins, rwidth=1)
        axes.set_xlabel('Smooth index')
        axes.set_ylabel('Num. SNPs')
        axes.set_xlim(xmin2d, xmax2d)
        ymin, ymax = axes.get_ylim()
        axes.vlines(self.smooth_threhsold, ymin, ymax, color='r')

        axes = divider.append_axes('left', size=2, pad=0.1, sharey=axes2)
        #axes = fig.add_subplot(221)
        axes.hist(y, orientation='horizontal', fill=True, log=True, bins=bins,
                  rwidth=1)
        axes.set_ylabel('Num. recombs.')
        axes.set_xlabel('Num. SNPs')
        _print_figure(axes, fig, fhand, plot_legend=False)
        axes.set_ylim(ymin2d, ymax2d)
        xmin, xmax = axes.get_xlim()
        if self.recomb_threshold is not None:
            axes.hlines(self.recomb_threshold, xmin, xmax, color='r')