Example #1
0
    def plotAll(self,
                timer,
                coreCut,
                transform=True,
                ignoreContigLengths=False):
        """Plot all contigs over a certain length which are unbinned"""
        self.loadData(timer, "((length >= " + str(coreCut) + "))")
        if transform:
            self.transformCP(timer)
        else:
            if self.numStoits == 3:
                self.transformedCP = self.covProfiles
            else:
                print("Number of stoits != 3. You need to transform")
                self.transformCP(timer)

        fig = plt.figure()
        ax1 = fig.add_subplot(111, projection='3d')
        if ignoreContigLengths:
            sc = ax1.scatter(self.transformedCP[:, 0],
                             self.transformedCP[:, 1],
                             self.transformedCP[:, 2],
                             edgecolors='none',
                             c=self.contigGCs,
                             cmap=self.colorMapGC,
                             vmin=0.0,
                             vmax=1.0,
                             marker='.',
                             s=10.)
        else:
            sc = ax1.scatter(self.transformedCP[:, 0],
                             self.transformedCP[:, 1],
                             self.transformedCP[:, 2],
                             edgecolors='k',
                             c=self.contigGCs,
                             cmap=self.colorMapGC,
                             vmin=0.0,
                             vmax=1.0,
                             marker='.',
                             s=np_sqrt(self.contigLengths))

        sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect
        self.plotStoitNames(ax1)

        cbar = plt.colorbar(sc, shrink=0.5)
        cbar.ax.tick_params()
        cbar.ax.set_title("% GC", size=10)
        cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
        #import IPython; IPython.embed()
        cbar.ax.set_ylim([0.15, 0.85])
        mungeCbar(cbar)

        try:
            plt.show()
            plt.close(fig)
        except:
            print("Error showing image", exc_info()[0])
            raise
        del fig
Example #2
0
    def plotAll(self, timer, coreCut, transform=True, ignoreContigLengths=False):
        """Plot all contigs over a certain length which are unbinned"""
        self.loadData(timer, "((length >= "+str(coreCut)+"))")
        if transform:
            self.transformCP(timer)
        else:
            if self.numStoits == 3:
                self.transformedCP = self.covProfiles
            else:
                print "Number of stoits != 3. You need to transform"
                self.transformCP(timer)

        fig = plt.figure()
        ax1 = fig.add_subplot(111, projection='3d')
        if ignoreContigLengths:
            sc = ax1.scatter(self.transformedCP[:,0],
                             self.transformedCP[:,1],
                             self.transformedCP[:,2],
                             edgecolors='none',
                             c=self.contigGCs,
                             cmap=self.colorMapGC,
                             vmin=0.0,
                             vmax=1.0,
                             marker='.',
                             s=10.
                             )
        else:
            sc = ax1.scatter(self.transformedCP[:,0],
                             self.transformedCP[:,1],
                             self.transformedCP[:,2],
                             edgecolors='k',
                             c=self.contigGCs,
                             cmap=self.colorMapGC,
                             vmin=0.0,
                             vmax=1.0,
                             marker='.',
                             s=np_sqrt(self.contigLengths)
                             )

        sc.set_edgecolors = sc.set_facecolors = lambda *args:None  # disable depth transparency effect
        self.plotStoitNames(ax1)

        cbar = plt.colorbar(sc, shrink=0.5)
        cbar.ax.tick_params()
        cbar.ax.set_title("% GC", size=10)
        cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
        #import IPython; IPython.embed()
        cbar.ax.set_ylim([0.15, 0.85])
        mungeCbar(cbar)

        try:
            plt.show()
            plt.close(fig)
        except:
            print "Error showing image", exc_info()[0]
            raise
        del fig
Example #3
0
    def renderTransCPData(self,
                          fileName="",
                          show=True,
                          elev=45,
                          azim=45,
                          all=False,
                          showAxis=False,
                          primaryWidth=12,
                          primarySpace=3,
                          dpi=300,
                          format='png',
                          fig=None,
                          highlight=None,
                          restrictedBids=[],
                          alpha=1,
                          ignoreContigLengths=False):
        """Plot transformed data in 3D"""
        del_fig = False
        if (fig is None):
            fig = plt.figure()
            del_fig = True
        else:
            plt.clf()
        if (all):
            myAXINFO = {
                'x': {
                    'i': 0,
                    'tickdir': 1,
                    'juggled': (1, 0, 2),
                    'color': (0, 0, 0, 0, 0)
                },
                'y': {
                    'i': 1,
                    'tickdir': 0,
                    'juggled': (0, 1, 2),
                    'color': (0, 0, 0, 0, 0)
                },
                'z': {
                    'i': 2,
                    'tickdir': 0,
                    'juggled': (0, 2, 1),
                    'color': (0, 0, 0, 0, 0)
                },
            }

            ax = fig.add_subplot(131, projection='3d')
            sc = ax.scatter(self.transformedCP[:, 0],
                            self.transformedCP[:, 1],
                            self.transformedCP[:, 2],
                            edgecolors='k',
                            c=self.contigGCs,
                            cmap=self.colorMapGC,
                            vmin=0.0,
                            vmax=1.0,
                            marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect
            ax.azim = 0
            ax.elev = 0
            ax.set_xlim3d(0, self.scaleFactor)
            ax.set_ylim3d(0, self.scaleFactor)
            ax.set_zlim3d(0, self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            for axis in ax.w_xaxis, ax.w_yaxis, ax.w_zaxis:
                for elt in axis.get_ticklines() + axis.get_ticklabels():
                    elt.set_visible(False)
            ax.w_xaxis._AXINFO = myAXINFO
            ax.w_yaxis._AXINFO = myAXINFO
            ax.w_zaxis._AXINFO = myAXINFO

            ax = fig.add_subplot(132, projection='3d')
            sc = ax.scatter(self.transformedCP[:, 0],
                            self.transformedCP[:, 1],
                            self.transformedCP[:, 2],
                            edgecolors='k',
                            c=self.contigGCs,
                            cmap=self.colorMapGC,
                            vmin=0.0,
                            vmax=1.0,
                            marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect
            ax.azim = 90
            ax.elev = 0
            ax.set_xlim3d(0, self.scaleFactor)
            ax.set_ylim3d(0, self.scaleFactor)
            ax.set_zlim3d(0, self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            for axis in ax.w_xaxis, ax.w_yaxis, ax.w_zaxis:
                for elt in axis.get_ticklines() + axis.get_ticklabels():
                    elt.set_visible(False)
            ax.w_xaxis._AXINFO = myAXINFO
            ax.w_yaxis._AXINFO = myAXINFO
            ax.w_zaxis._AXINFO = myAXINFO

            ax = fig.add_subplot(133, projection='3d')
            sc = ax.scatter(self.transformedCP[:, 0],
                            self.transformedCP[:, 1],
                            self.transformedCP[:, 2],
                            edgecolors='k',
                            c=self.contigGCs,
                            cmap=self.colorMapGC,
                            vmin=0.0,
                            vmax=1.0,
                            marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect
            ax.azim = 0
            ax.elev = 90
            ax.set_xlim3d(0, self.scaleFactor)
            ax.set_ylim3d(0, self.scaleFactor)
            ax.set_zlim3d(0, self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            for axis in ax.w_xaxis, ax.w_yaxis, ax.w_zaxis:
                for elt in axis.get_ticklines() + axis.get_ticklabels():
                    elt.set_visible(False)
            ax.w_xaxis._AXINFO = myAXINFO
            ax.w_yaxis._AXINFO = myAXINFO
            ax.w_zaxis._AXINFO = myAXINFO
        else:
            ax = fig.add_subplot(111, projection='3d')
            if len(restrictedBids) == 0:
                if highlight is None:
                    print("BF:", np_shape(self.transformedCP))
                    if ignoreContigLengths:
                        sc = ax.scatter(self.transformedCP[:, 0],
                                        self.transformedCP[:, 1],
                                        self.transformedCP[:, 2],
                                        edgecolors='none',
                                        c=self.contigGCs,
                                        cmap=self.colorMapGC,
                                        s=10.,
                                        vmin=0.0,
                                        vmax=1.0,
                                        marker='.')
                    else:
                        sc = ax.scatter(self.transformedCP[:, 0],
                                        self.transformedCP[:, 1],
                                        self.transformedCP[:, 2],
                                        edgecolors='none',
                                        c=self.contigGCs,
                                        cmap=self.colorMapGC,
                                        vmin=0.0,
                                        vmax=1.0,
                                        s=np_sqrt(self.contigLengths),
                                        marker='.')
                    sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect
                else:
                    #draw the opaque guys first
                    """
                    sc = ax.scatter(self.transformedCP[:,0],
                                    self.transformedCP[:,1],
                                    self.transformedCP[:,2],
                                    edgecolors='none',
                                    c=self.contigGCs,
                                    cmap=self.colorMapGC,
                                    vmin=0.0,
                                    vmax=1.0,
                                    s=100.,
                                    marker='s',
                                    alpha=alpha)
                    sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect
                    """
                    # now replot the highlighted guys
                    disp_vals = np_array([])
                    disp_GCs = np_array([])

                    thrower = {}
                    hide_vals = np_array([])
                    hide_GCs = np_array([])

                    num_points = 0
                    for bin in highlight:
                        for row_index in bin.rowIndices:
                            num_points += 1
                            disp_vals = np_append(
                                disp_vals, self.transformedCP[row_index])
                            disp_GCs = np_append(disp_GCs,
                                                 self.contigGCs[row_index])
                            thrower[row_index] = False
                    # reshape
                    disp_vals = np_reshape(disp_vals, (num_points, 3))

                    num_points = 0
                    for i in range(len(self.indices)):
                        try:
                            thrower[i]
                        except KeyError:
                            num_points += 1
                            hide_vals = np_append(hide_vals,
                                                  self.transformedCP[i])
                            hide_GCs = np_append(hide_GCs, self.contigGCs[i])
                    # reshape
                    hide_vals = np_reshape(hide_vals, (num_points, 3))

                    sc = ax.scatter(hide_vals[:, 0],
                                    hide_vals[:, 1],
                                    hide_vals[:, 2],
                                    edgecolors='none',
                                    c=hide_GCs,
                                    cmap=self.colorMapGC,
                                    vmin=0.0,
                                    vmax=1.0,
                                    s=100.,
                                    marker='s',
                                    alpha=alpha)
                    sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect

                    sc = ax.scatter(disp_vals[:, 0],
                                    disp_vals[:, 1],
                                    disp_vals[:, 2],
                                    edgecolors='none',
                                    c=disp_GCs,
                                    cmap=self.colorMapGC,
                                    vmin=0.0,
                                    vmax=1.0,
                                    s=10.,
                                    marker='.')
                    sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect

                    print(np_shape(disp_vals), np_shape(hide_vals),
                          np_shape(self.transformedCP))

                # render color bar
                cbar = plt.colorbar(sc, shrink=0.5)
                cbar.ax.tick_params()
                cbar.ax.set_title("% GC", size=10)
                cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
                cbar.ax.set_ylim([0.15, 0.85])
                mungeCbar(cbar)
            else:
                r_trans = np_array([])
                r_cols = np_array([])
                num_added = 0
                for i in range(len(self.indices)):
                    if self.binIds[i] not in restrictedBids:
                        r_trans = np_append(r_trans, self.transformedCP[i])
                        r_cols = np_append(r_cols, self.contigGCs[i])
                        num_added += 1
                r_trans = np_reshape(r_trans, (num_added, 3))
                print(np_shape(r_trans))
                #r_cols = np_reshape(r_cols, (num_added,3))
                sc = ax.scatter(r_trans[:, 0],
                                r_trans[:, 1],
                                r_trans[:, 2],
                                edgecolors='none',
                                c=r_cols,
                                cmap=self.colorMapGC,
                                s=10.,
                                vmin=0.0,
                                vmax=1.0,
                                marker='.')
                sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect

                # render color bar
                cbar = plt.colorbar(sc, shrink=0.5)
                cbar.ax.tick_params()
                cbar.ax.set_title("% GC", size=10)
                cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
                cbar.ax.set_ylim([0.15, 0.85])
                mungeCbar(cbar)

            ax.azim = azim
            ax.elev = elev
            ax.set_xlim3d(0, self.scaleFactor)
            ax.set_ylim3d(0, self.scaleFactor)
            ax.set_zlim3d(0, self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            if (not showAxis):
                ax.set_axis_off()

        if (fileName != ""):
            try:
                if (all):
                    fig.set_size_inches(3 * primaryWidth + 2 * primarySpace,
                                        primaryWidth)
                else:
                    fig.set_size_inches(primaryWidth, primaryWidth)
                plt.savefig(fileName, dpi=dpi, format=format)
            except:
                print("Error saving image", fileName, exc_info()[0])
                raise
        elif (show):
            try:
                plt.show()
            except:
                print("Error showing image", exc_info()[0])
                raise
        if del_fig:
            plt.close(fig)
            del fig
Example #4
0
    def r2nderTransCPData(
        self,
        fig,
        alphaIndices=[],
        visibleIndices=[],
        alpha=1,
        ignoreContigLengths=False,
        elev=45,
        azim=45,
        fileName="",
        dpi=300,
        format='png',
        primaryWidth=6,
        title="",
        showAxis=False,
        showColorbar=True,
    ):
        """Plot transformed data in 3D"""
        # clear any existing plot
        plt.clf()
        ax = fig.add_subplot(111, projection='3d')

        # work out the coords an colours based on indices
        alpha_coords = self.transformedCP[alphaIndices]
        alpha_GCs = self.contigGCs[alphaIndices]
        visible_coords = self.transformedCP[visibleIndices]
        visible_GCs = self.contigGCs[visibleIndices]

        # lengths if needed
        if not ignoreContigLengths:
            alpha_lengths = self.contigLengths[alphaIndices]
            visible_lengths = self.contigLengths[visibleIndices]
        else:
            alpha_lengths = 10.
            visible_lengths = 10.

        # first plot alpha points
        if len(alpha_GCs) > 0:
            sc = ax.scatter(alpha_coords[:, 0],
                            alpha_coords[:, 1],
                            alpha_coords[:, 2],
                            edgecolors='none',
                            c=alpha_GCs,
                            cmap=self.colorMapGC,
                            vmin=0.0,
                            vmax=1.0,
                            s=alpha_lengths,
                            marker='.',
                            alpha=alpha)
            sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect

        # then plot full visible points
        if len(visible_GCs) > 0:
            sc = ax.scatter(visible_coords[:, 0],
                            visible_coords[:, 1],
                            visible_coords[:, 2],
                            edgecolors='none',
                            c=visible_GCs,
                            cmap=self.colorMapGC,
                            s=visible_lengths,
                            vmin=0.0,
                            vmax=1.0,
                            marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args: None  # disable depth transparency effect

        # render color bar
        if showColorbar:
            cbar = plt.colorbar(sc, shrink=0.5)
            cbar.ax.tick_params()
            cbar.ax.set_title("% GC", size=10)
            cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
            cbar.ax.set_ylim([0.15, 0.85])
            mungeCbar(cbar)

        # set aspect
        ax.azim = azim
        ax.elev = elev

        # make it purdy
        ax.set_xlim3d(0, self.scaleFactor)
        ax.set_ylim3d(0, self.scaleFactor)
        ax.set_zlim3d(0, self.scaleFactor)
        ax.set_xticklabels([])
        ax.set_yticklabels([])
        ax.set_zticklabels([])
        ax.set_xticks([])
        ax.set_yticks([])
        ax.set_zticks([])

        plt.tight_layout()

        if title != "":
            plt.title(title)

        if (not showAxis):
            ax.set_axis_off()

        if (fileName != ""):
            try:
                fig.set_size_inches(primaryWidth, primaryWidth)
                plt.savefig(fileName, dpi=dpi, format=format)
            except:
                print("Error saving image", fileName, exc_info()[0])
                raise
        else:
            try:
                plt.show()
            except:
                print("Error showing image", exc_info()[0])
                raise
Example #5
0
    def r2nderTransCPData(self,
                          fig,
                          alphaIndices=[],
                          visibleIndices=[],
                          alpha=1,
                          ignoreContigLengths=False,
                          elev=45,
                          azim=45,
                          fileName="",
                          dpi=300,
                          format='png',
                          primaryWidth=6,
                          title="",
                          showAxis=False,
                          showColorbar=True,):
        """Plot transformed data in 3D"""
        # clear any existing plot
        plt.clf()
        ax = fig.add_subplot(111, projection='3d')

        # work out the coords an colours based on indices
        alpha_coords = self.transformedCP[alphaIndices]
        alpha_GCs = self.contigGCs[alphaIndices]
        visible_coords = self.transformedCP[visibleIndices]
        visible_GCs = self.contigGCs[visibleIndices]

        # lengths if needed
        if not ignoreContigLengths:
            alpha_lengths = self.contigLengths[alphaIndices]
            visible_lengths = self.contigLengths[visibleIndices]
        else:
            alpha_lengths = 10.
            visible_lengths = 10.

        # first plot alpha points
        if len(alpha_GCs) > 0:
            sc = ax.scatter(alpha_coords[:,0],
                            alpha_coords[:,1],
                            alpha_coords[:,2],
                            edgecolors='none',
                            c=alpha_GCs,
                            cmap=self.colorMapGC,
                            vmin=0.0,
                            vmax=1.0,
                            s=alpha_lengths,
                            marker='.',
                            alpha=alpha)
            sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect

        # then plot full visible points
        if len(visible_GCs) > 0:
            sc = ax.scatter(visible_coords[:,0],
                            visible_coords[:,1],
                            visible_coords[:,2],
                            edgecolors='none',
                            c=visible_GCs,
                            cmap=self.colorMapGC,
                            s=visible_lengths,
                            vmin=0.0,
                            vmax=1.0,
                            marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect

        # render color bar
        if showColorbar:
            cbar = plt.colorbar(sc, shrink=0.5)
            cbar.ax.tick_params()
            cbar.ax.set_title("% GC", size=10)
            cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
            cbar.ax.set_ylim([0.15, 0.85])
            mungeCbar(cbar)

        # set aspect
        ax.azim = azim
        ax.elev = elev

        # make it purdy
        ax.set_xlim3d(0,self.scaleFactor)
        ax.set_ylim3d(0,self.scaleFactor)
        ax.set_zlim3d(0,self.scaleFactor)
        ax.set_xticklabels([])
        ax.set_yticklabels([])
        ax.set_zticklabels([])
        ax.set_xticks([])
        ax.set_yticks([])
        ax.set_zticks([])

        plt.tight_layout()

        if title != "":
            plt.title(title)

        if(not showAxis):
            ax.set_axis_off()

        if(fileName != ""):
            try:
                fig.set_size_inches(primaryWidth,primaryWidth)
                plt.savefig(fileName,dpi=dpi,format=format)
            except:
                print "Error saving image",fileName, exc_info()[0]
                raise
        else:
            try:
                plt.show()
            except:
                print "Error showing image", exc_info()[0]
                raise
Example #6
0
    def renderTransCPData(self,
                          fileName="",
                          show=True,
                          elev=45,
                          azim=45,
                          all=False,
                          showAxis=False,
                          primaryWidth=12,
                          primarySpace=3,
                          dpi=300,
                          format='png',
                          fig=None,
                          highlight=None,
                          restrictedBids=[],
                          alpha=1,
                          ignoreContigLengths=False):
        """Plot transformed data in 3D"""
        del_fig = False
        if(fig is None):
            fig = plt.figure()
            del_fig = True
        else:
            plt.clf()
        if(all):
            myAXINFO = {
                'x': {'i': 0, 'tickdir': 1, 'juggled': (1, 0, 2),
                'color': (0, 0, 0, 0, 0)},
                'y': {'i': 1, 'tickdir': 0, 'juggled': (0, 1, 2),
                'color': (0, 0, 0, 0, 0)},
                'z': {'i': 2, 'tickdir': 0, 'juggled': (0, 2, 1),
                'color': (0, 0, 0, 0, 0)},
            }

            ax = fig.add_subplot(131, projection='3d')
            sc = ax.scatter(self.transformedCP[:,0], self.transformedCP[:,1], self.transformedCP[:,2], edgecolors='k', c=self.contigGCs, cmap=self.colorMapGC, vmin=0.0, vmax=1.0, marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args:None  # disable depth transparency effect
            ax.azim = 0
            ax.elev = 0
            ax.set_xlim3d(0,self.scaleFactor)
            ax.set_ylim3d(0,self.scaleFactor)
            ax.set_zlim3d(0,self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            for axis in ax.w_xaxis, ax.w_yaxis, ax.w_zaxis:
                for elt in axis.get_ticklines() + axis.get_ticklabels():
                    elt.set_visible(False)
            ax.w_xaxis._AXINFO = myAXINFO
            ax.w_yaxis._AXINFO = myAXINFO
            ax.w_zaxis._AXINFO = myAXINFO

            ax = fig.add_subplot(132, projection='3d')
            sc = ax.scatter(self.transformedCP[:,0], self.transformedCP[:,1], self.transformedCP[:,2], edgecolors='k', c=self.contigGCs, cmap=self.colorMapGC, vmin=0.0, vmax=1.0, marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args:None  # disable depth transparency effect
            ax.azim = 90
            ax.elev = 0
            ax.set_xlim3d(0,self.scaleFactor)
            ax.set_ylim3d(0,self.scaleFactor)
            ax.set_zlim3d(0,self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            for axis in ax.w_xaxis, ax.w_yaxis, ax.w_zaxis:
                for elt in axis.get_ticklines() + axis.get_ticklabels():
                    elt.set_visible(False)
            ax.w_xaxis._AXINFO = myAXINFO
            ax.w_yaxis._AXINFO = myAXINFO
            ax.w_zaxis._AXINFO = myAXINFO

            ax = fig.add_subplot(133, projection='3d')
            sc = ax.scatter(self.transformedCP[:,0], self.transformedCP[:,1], self.transformedCP[:,2], edgecolors='k', c=self.contigGCs, cmap=self.colorMapGC, vmin=0.0, vmax=1.0, marker='.')
            sc.set_edgecolors = sc.set_facecolors = lambda *args:None  # disable depth transparency effect
            ax.azim = 0
            ax.elev = 90
            ax.set_xlim3d(0,self.scaleFactor)
            ax.set_ylim3d(0,self.scaleFactor)
            ax.set_zlim3d(0,self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            for axis in ax.w_xaxis, ax.w_yaxis, ax.w_zaxis:
                for elt in axis.get_ticklines() + axis.get_ticklabels():
                    elt.set_visible(False)
            ax.w_xaxis._AXINFO = myAXINFO
            ax.w_yaxis._AXINFO = myAXINFO
            ax.w_zaxis._AXINFO = myAXINFO
        else:
            ax = fig.add_subplot(111, projection='3d')
            if len(restrictedBids) == 0:
                if highlight is None:
                    print "BF:", np_shape(self.transformedCP)
                    if ignoreContigLengths:
                        sc = ax.scatter(self.transformedCP[:,0],
                                   self.transformedCP[:,1],
                                   self.transformedCP[:,2],
                                   edgecolors='none',
                                   c=self.contigGCs,
                                   cmap=self.colorMapGC,
                                   s=10.,
                                   vmin=0.0,
                                   vmax=1.0,
                                   marker='.')
                    else:
                        sc = ax.scatter(self.transformedCP[:,0],
                                   self.transformedCP[:,1],
                                   self.transformedCP[:,2],
                                   edgecolors='none',
                                   c=self.contigGCs,
                                   cmap=self.colorMapGC,
                                   vmin=0.0,
                                   vmax=1.0,
                                   s=np_sqrt(self.contigLengths),
                                   marker='.')
                    sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect
                else:
                    #draw the opaque guys first
                    """
                    sc = ax.scatter(self.transformedCP[:,0],
                                    self.transformedCP[:,1],
                                    self.transformedCP[:,2],
                                    edgecolors='none',
                                    c=self.contigGCs,
                                    cmap=self.colorMapGC,
                                    vmin=0.0,
                                    vmax=1.0,
                                    s=100.,
                                    marker='s',
                                    alpha=alpha)
                    sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect
                    """
                    # now replot the highlighted guys
                    disp_vals = np_array([])
                    disp_GCs = np_array([])

                    thrower = {}
                    hide_vals = np_array([])
                    hide_GCs = np_array([])

                    num_points = 0
                    for bin in highlight:
                        for row_index in bin.rowIndices:
                            num_points += 1
                            disp_vals = np_append(disp_vals, self.transformedCP[row_index])
                            disp_GCs = np_append(disp_GCs, self.contigGCs[row_index])
                            thrower[row_index] = False
                    # reshape
                    disp_vals = np_reshape(disp_vals, (num_points, 3))

                    num_points = 0
                    for i in range(len(self.indices)):
                        try:
                            thrower[i]
                        except KeyError:
                            num_points += 1
                            hide_vals = np_append(hide_vals, self.transformedCP[i])
                            hide_GCs = np_append(hide_GCs, self.contigGCs[i])
                    # reshape
                    hide_vals = np_reshape(hide_vals, (num_points, 3))

                    sc = ax.scatter(hide_vals[:,0],
                                    hide_vals[:,1],
                                    hide_vals[:,2],
                                    edgecolors='none',
                                    c=hide_GCs,
                                    cmap=self.colorMapGC,
                                    vmin=0.0,
                                    vmax=1.0,
                                    s=100.,
                                    marker='s',
                                    alpha=alpha)
                    sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect

                    sc = ax.scatter(disp_vals[:,0],
                                    disp_vals[:,1],
                                    disp_vals[:,2],
                                    edgecolors='none',
                                    c=disp_GCs,
                                    cmap=self.colorMapGC,
                                    vmin=0.0,
                                    vmax=1.0,
                                    s=10.,
                                    marker='.')
                    sc.set_edgecolors = sc.set_facecolors = lambda *args:None # disable depth transparency effect

                    print np_shape(disp_vals), np_shape(hide_vals), np_shape(self.transformedCP)

                # render color bar
                cbar = plt.colorbar(sc, shrink=0.5)
                cbar.ax.tick_params()
                cbar.ax.set_title("% GC", size=10)
                cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
                cbar.ax.set_ylim([0.15, 0.85])
                mungeCbar(cbar)
            else:
                r_trans = np_array([])
                r_cols=np_array([])
                num_added = 0
                for i in range(len(self.indices)):
                    if self.binIds[i] not in restrictedBids:
                        r_trans = np_append(r_trans, self.transformedCP[i])
                        r_cols = np_append(r_cols, self.contigGCs[i])
                        num_added += 1
                r_trans = np_reshape(r_trans, (num_added,3))
                print np_shape(r_trans)
                #r_cols = np_reshape(r_cols, (num_added,3))
                sc = ax.scatter(r_trans[:,0],
                                r_trans[:,1],
                                r_trans[:,2],
                                edgecolors='none',
                                c=r_cols,
                                cmap=self.colorMapGC,
                                s=10.,
                                vmin=0.0,
                                vmax=1.0,
                                marker='.')
                sc.set_edgecolors = sc.set_facecolors = lambda *args:None  # disable depth transparency effect

                # render color bar
                cbar = plt.colorbar(sc, shrink=0.5)
                cbar.ax.tick_params()
                cbar.ax.set_title("% GC", size=10)
                cbar.set_ticks([0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8])
                cbar.ax.set_ylim([0.15, 0.85])
                mungeCbar(cbar)

            ax.azim = azim
            ax.elev = elev
            ax.set_xlim3d(0,self.scaleFactor)
            ax.set_ylim3d(0,self.scaleFactor)
            ax.set_zlim3d(0,self.scaleFactor)
            ax.set_xticklabels([])
            ax.set_yticklabels([])
            ax.set_zticklabels([])
            ax.set_xticks([])
            ax.set_yticks([])
            ax.set_zticks([])
            if(not showAxis):
                ax.set_axis_off()

        if(fileName != ""):
            try:
                if(all):
                    fig.set_size_inches(3*primaryWidth+2*primarySpace,primaryWidth)
                else:
                    fig.set_size_inches(primaryWidth,primaryWidth)
                plt.savefig(fileName,dpi=dpi,format=format)
            except:
                print "Error saving image",fileName, exc_info()[0]
                raise
        elif(show):
            try:
                plt.show()
            except:
                print "Error showing image", exc_info()[0]
                raise
        if del_fig:
            plt.close(fig)
            del fig