Change to the collate estimate category script

RPGroup-PBoC · Oct 18, 2020 · 171aadf · 171aadf
1 parent 908b089
commit 171aadf
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Showing 3 changed files with 152 additions and 152 deletions.
diff --git a/code/figures/fig8bc_RNA_synthesis.py b/code/figures/fig8bc_RNA_synthesis.py
@@ -31,7 +31,7 @@
 L_rRNA = 4500
 r_txn = 40 # in nt/s
 n_operon = 7
-footprint = 80 # in nt
+footprint = 40 # in nt
 n_tRNA = theta_prot * theta_dry * cell_mass / (m_aa * t_double)
 L_tRNA = 80
 
@@ -41,7 +41,7 @@
 #%%
 fig, ax = plt.subplots(1, 2, figsize=(6.5, 2.5))
 for a in ax:
-    a.plot(growth_rate, N_polymerase, '-', lw=3, color='grey', alpha=0.4, label='replication fork scaling')
+    a.plot(growth_rate, N_polymerase, '-', lw=3, color='grey', alpha=0.4, label='scaling with DNA content')
     a.set_xlabel('growth rate [hr$^{-1}$]', fontsize=8)
     a.set_yscale('log')
     a.set_xlim([0, 2])
@@ -54,9 +54,9 @@
 
 # Plot the predictions
 for a in ax:
-    a.plot(0.5, 1E3, 'o', ms=6, alpha=0.4, color=colors['dark_brown'], label='estimated value')
-    a.vlines(0.5, 1, 1E3, color='k', linestyle='--', label='__nolegend__', lw=0.75)
-    a.hlines(1E3, 0, 0.5, color='k', linestyle='--', label='__nolegend__', lw=0.75)
+    a.plot(0.5, 1.5E3, 'o', ms=6, alpha=0.4, color=colors['dark_brown'], label='estimated value')
+    a.vlines(0.5, 1, 1.5E3, color='k', linestyle='--', label='__nolegend__', lw=0.75)
+    a.hlines(1.5E3, 0, 0.5, color='k', linestyle='--', label='__nolegend__', lw=0.75)
 
 # plot the data
 for p, a in zip([rnap, sig70], ax.ravel()):

diff --git a/code/processing/collation/collate_estimate_categories.py b/code/processing/collation/collate_estimate_categories.py
@@ -33,13 +33,13 @@
                        'gene_name': ['rpoD'],
                        'rate_per_sec': np.nan,
                        'units': 'none',
-                       'method': 'no aggregation',
+                       'method': 'sum',
                        'category':'synthesis'},
             'all_sigma': {'name': 'all σ-factors',
                           'gene_name': ['rpoE', 'fecI', 'rpoF', 'rpoH', 'rpoN', 'rpoD', 'rpoS'],
                           'rate_per_sec': np.nan,
                           'units':'none',
-                          'method':'no aggregation',
+                          'method':'sum',
                           'category':'synthesis'},
              'trna': {'name': 'tRNA ligases',
                       'go_terms': ['GO:0006419', 'GO:0006420', 'GO:0006421',
@@ -118,7 +118,7 @@
                      'method': 'sum',
                      'rate_per_sec': np.nan,
                      'units':'none',
-                     'category':'no aggregation'},
+                     'category':'sum'},
             'atp_synthase': {'name': 'F1-F0 ATP Synthase',
                             'complexes':  ['ATPSYN-CPLX'],
                             'method': 'sum',