diff --git a/bin/MutaRNA-plot.py b/bin/MutaRNA-plot.py index 8c60f78..38fca98 100644 --- a/bin/MutaRNA-plot.py +++ b/bin/MutaRNA-plot.py @@ -291,10 +291,10 @@ def plot_up_dict(up_dic, plot_lims=None, title='XX', fig=None, diff=False,tidy=F ticks_label_step = 50 ticks_step = 10 - minor_ticks = np.arange(min(x), max(x), 1) + minor_ticks = np.arange(min(x), max(x), 10) major_ticks = np.arange(min(x)-min(x)%ticks_step, max(x), ticks_step) - ax.set_xticks(minor_ticks, minor=True) + #ax.set_xticks(minor_ticks, minor=True) ax.set_xticks(major_ticks) @@ -310,11 +310,11 @@ def plot_up_dict(up_dic, plot_lims=None, title='XX', fig=None, diff=False,tidy=F # ax.grid(which='both') # or if you want different settings for the grids: - ax.grid(which='minor', alpha=0.5) + ax.grid(which='major', axis='x', alpha=0.5) ax.axhline(0) if mutation_pos is not None: - ax.axvline(mutation_pos-0.5, color='r', alpha=0.5) + ax.axvline(mutation_pos, color='r', alpha=0.3, linestyle='--') # ax.axhline(0, linestyle='--', color='k', alpha=0.5) # horizontal lines # ax.axhline(1, linestyle='--', color='k', alpha=0.5) # horizontal lines @@ -331,11 +331,11 @@ def plot_up_dict(up_dic, plot_lims=None, title='XX', fig=None, diff=False,tidy=F - if ticks_label_step != ticks_step: - labels = [item.get_text() for item in ax.get_xticklabels()] - labels_locs = ax.get_xticks() - pruned_labels = [str(loc) if ((loc%ticks_label_step)==0 and loc!=0) else '' for loc, lab in zip(labels_locs, labels)] - ax.set_xticklabels(pruned_labels) + #if ticks_label_step != ticks_step: + labels = [item.get_text() for item in ax.get_xticklabels()] + labels_locs = ax.get_xticks() + pruned_labels = [str(loc) if ((loc%ticks_label_step)==0 and loc!=0) else '' for loc, lab in zip(labels_locs, labels)] + ax.set_xticklabels(pruned_labels) @@ -559,7 +559,7 @@ def plot_circos_seq_SNP(rec_wild, SNP_tag, rec_mut, do_local=True,do_global=Fals #ldp.plot_heat_maps(None, ldp.parse_dp_ps(dpintroduce), filename=ID+'-INTRODUCED', title_suffix=ID+'-INTRODUCED', what='basepairs',inverse=True, out_dir=out_dir) ldp.plot_heat_maps(None, ldp.parse_dp_ps(dp_wild)+ldp.parse_dp_ps(dp_mut).transpose(), filename=ID+'-WT-MUT', what='basepairs', - inverse=True, interactive=False, gene_loc=None,title_suffix=ID+'-'+SNP_tag+'\n'r'$P({\rm WT})$, $P({\rm mutant})$', out_dir=out_dir, upper_triangle_txt='wt',lower_triangle_txt='mut', mutation_pos=snp_loc) + inverse=True, interactive=False, gene_loc=None,title_suffix=ID+'-'+SNP_tag+'\n'r'$P({\rm WT})$, $P({\rm mutant})$', out_dir=out_dir, upper_triangle_txt='WT',lower_triangle_txt='MUT', mutation_pos=snp_loc) ldp.plot_heat_maps(None, ldp.parse_dp_ps(dpremove)+ldp.parse_dp_ps(dpintroduce).transpose(), filename=ID+'-REMOVED-INTRODUCED', what='basepairs', inverse=True, interactive=False, gene_loc=None,title_suffix=ID+'\n'+r'$|\Delta| = |P({\rm WT})-P({\rm mutant})|$', out_dir=out_dir, upper_triangle_txt='weakened\n' + r' $\Delta>0$',lower_triangle_txt='increased\n' + r' $\Delta<0$', mutation_pos=snp_loc) diff --git a/lib/local_dotplot/local_dotplot_lib.py b/lib/local_dotplot/local_dotplot_lib.py index c3d94a5..61d45a5 100644 --- a/lib/local_dotplot/local_dotplot_lib.py +++ b/lib/local_dotplot/local_dotplot_lib.py @@ -257,38 +257,46 @@ def my_heatmap(mat, fig, ax, title='', vmin=1e-2,vmax=1.0, inverse=True, interac # plt.colorbar(heatmap) ax.set_title(title) - incrementticks = np.arange(0, mat.shape[0], 1) + incrementticks = np.arange(0, mat.shape[0], 10)-1 ax.set_xticks(incrementticks) ax.set_yticks(incrementticks) - ticks = np.arange(0, mat.shape[0], 10) - #ax.set_xticks(ticks-0.5, minor=True) - #ax.set_yticks(ticks-0.5, minor=True) -# ax.grid(True, which='minor',color='gray',linewidth=0.0001 ) - ax.grid(False, which='major') # ,color='gray',linewidth=0.001 ) - # ax.gca().patch.set_facecolor('0.8') - # ax.tick_params(length=0, - # axis='both', # changes apply to the x-axis - # which='major', # 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') + ticks = np.arange(0, mat.shape[0], 50)-1 + ax.set_xticks(ticks, minor=True) + ax.set_yticks(ticks, minor=True) + ax.grid(True, which='minor' ,color='gray',linewidth=0.05,alpha=0.3 ) + +# ax.grid(True, which='minor',color='gray',linewidth=0.0001 ) + # ax.gca().patch.set_facecolor('0.8') + prune_labels = True ticks_label_step = 10 + if seq_len > 101: + ticks_label_step = 50 if prune_labels == True: labels = [item.get_text() for item in ax.get_xticklabels()] labels_locs = ax.get_xticks() - pruned_labels = [str(loc) if ((loc%ticks_label_step)==0 and loc!=0) else '' for loc, lab in zip(labels_locs, labels)] + pruned_labels = [str(int(loc+1)) if (((loc+1)%ticks_label_step)==0 and (loc+0.5)!=0) else '' for loc, lab in zip(labels_locs, labels)] ax.set_xticklabels(pruned_labels) # ax.set_xticks = [l-0.5 for l in labels_locs] labels = [item.get_text() for item in ax.get_yticklabels()] labels_locs = ax.get_yticks() - pruned_labels = [str(loc) if ((loc%ticks_label_step)==0 and loc!=0) else '' for loc, lab in zip(labels_locs, labels)] + pruned_labels = [str(int(loc+1)) if (((loc+1)%ticks_label_step)==0 and (loc+0.5)!=0) else '' for loc, lab in zip(labels_locs, labels)] ax.set_yticklabels(pruned_labels) # ax.set_yticks = [l-0.5 for l in labels_locs] + ax.tick_params(#length=0, + axis='both', # changes apply to the x-axis + which='major', # both major and minor ticks are affected + bottom=True, # ticks along the bottom edge are off + top=True, # ticks along the top edge are off + right=True, + labelbottom=True, + labeltop=False, + ) + ax.set_xlim((-0.5, seq_len-0.5)) # ax.set_ylim((-0.5,seq_len-0.5)) ax.set_ylim((seq_len-0.5, -0.5))