plot.py 文件源码

def _plot(self, region=None, cax=None):
        if region is None:
            raise ValueError("Cannot plot triangle plot for whole genome.")

        hm, sr = sub_matrix_regions(self.hic_matrix, self.regions, region)
        hm[np.tril_indices(hm.shape[0])] = np.nan
        # Remove part of matrix further away than max_dist
        if self.max_dist is not None:
            for i in range(hm.shape[0]):
                i_region = sr[i]
                for j in range(hm.shape[1]):
                    j_region = sr[j]

                    if j_region.start-i_region.end > self.max_dist:
                        hm[i, j] = np.nan

        hm_masked = np.ma.MaskedArray(hm, mask=np.isnan(hm))
        # prepare an array of the corner coordinates of the Hic-matrix
        # Distances have to be scaled by sqrt(2), because the diagonals of the bins
        # are sqrt(2)*len(bin_size)
        sqrt2 = math.sqrt(2)
        bin_coords = np.r_[[(x.start - 1) for x in sr], sr[-1].end]/sqrt2
        X, Y = np.meshgrid(bin_coords, bin_coords)
        # rotatate coordinate matrix 45 degrees
        sin45 = math.sin(math.radians(45))
        X_, Y_ = X*sin45 + Y*sin45, X*sin45 - Y*sin45
        # shift x coords to correct start coordinate and center the diagonal directly on the
        # x-axis
        X_ -= X_[1, 0] - (sr[0].start - 1)
        Y_ -= .5*np.min(Y_) + .5*np.max(Y_)
        # create plot
        self.hicmesh = self.ax.pcolormesh(X_, Y_, hm_masked, cmap=self.colormap, norm=self.norm)

        # set limits and aspect ratio
        #self.ax.set_aspect(aspect="equal")
        ylim_max = 0.5*(region.end-region.start)
        if self.max_dist is not None and self.max_dist/2 < ylim_max:
            ylim_max = self.max_dist/2
        self.ax.set_ylim(0, ylim_max)
        # remove y ticks
        self.ax.set_yticks([])
        # hide background patch
        self.ax.patch.set_visible(False)
        if self.show_colorbar:
            self.add_colorbar(cax)