def plot_pseudotime()

in poincare_maps.py [0:0]

• 44 lines of code
• 19 McCabe index (conditional complexity)

    def plot_pseudotime(self, data, markesnames, labels, file_name=None, fs=8, idx=[], pm_pseudotime=None,colors_dict=None):        
        if pm_pseudotime is None:
            pm_pseudotime = self.distances[self.iroot, :]

        if colors_dict is None:
            colors_dict = dict(zip(np.unique(labels), self.colors_palette[:len(np.unique(labels))]))
        
        if len(idx):
            # preserve global colors                            
            pm_pseudotime = pm_pseudotime[idx]
            data = data[idx, :]
            labels = labels[idx]

        n_plt = len(markesnames)
        # n2 = int(np.sqrt(n_plt))
        n2 = 3
        n1 = n_plt // n2

        if n1*n2 < n_plt:
            n1 += 1

        if n1 == 1:
            n1 = 2
        
        if n2 == 1:
            n2 = 2


        pl_size = 2
        fig, axs = plt.subplots(n1, n2, sharey=False, figsize=(n2*pl_size + 2, n1*pl_size))

        i = 0               

        for i1 in range(n1):
            for i2 in range(n2):
                axs[i1, i2].grid('off')
                axs[i1, i2].yaxis.set_tick_params(labelsize=fs)
                axs[i1, i2].xaxis.set_tick_params(labelsize=fs)
                if i < n_plt:
                    marker = markesnames[i]
                    for j, label in enumerate(np.unique(labels)):
                        idx = np.where(labels == label)[0]
                        axs[i1, i2].plot(pm_pseudotime[idx], data[idx, i], marker='o', markerfacecolor='none', c=colors_dict[label], linestyle='', ms=2, label=marker)                
                    axs[i1, i2].set_title(marker, fontsize=fs)
                    i += 1
                    if i == n_plt:
                        axs[i1, i2].legend(np.unique(labels), loc='center left', bbox_to_anchor=(1, 0.5), fontsize=fs)
                else:
                    axs[i1, i2].axis('off')
        axs[i1, i2].legend(np.unique(labels), loc='center left', bbox_to_anchor=(1, 0.5), fontsize=fs)
        
        # for ax in axs.flat:
        #   ax.set(xlabel='pseudotime')
        #   # Hide x labels and tick labels for top plots and y ticks for right plots.
        # for ax in axs.flat:
        #   ax.label_outer()

        plt.xlabel('pseudotime', fontsize=fs)
        fig.tight_layout()

        if file_name:
            plt.savefig(file_name + '.pdf', format='pdf')

        plt.show()
        plt.close(fig)