bamtools.py 文件源码

def plot_gc_content(self, fontsize=16, ec="k", bins=100):
        """plot GC content histogram

        :params bins: a value for the number of bins or an array (with a copy()
            method)
        :param ec: add black contour on the bars

        .. plot::
            :include-source:

            from sequana import BAM, sequana_data
            b = BAM(sequana_data('test.bam'))
            b.plot_gc_content()

        """
        data = self.get_gc_content()
        try:
            X = np.linspace(0, 100, bins)
        except:
            X = bins.copy()

        pylab.hist(data, X, normed=True, ec=ec)
        pylab.grid(True)
        mu = pylab.mean(data)
        sigma = pylab.std(data)

        X = pylab.linspace(X.min(), X.max(), 100)
        pylab.plot(X, pylab.normpdf(X, mu, sigma), lw=2, color="r", ls="--")
        pylab.xlabel("GC content", fontsize=16)