Make figure refs bold

kda_paper/README.md

@@ -25,7 +25,7 @@ This will create and store all figures for the 4-state model in the current work
 
 ### Figure 10: KDA Validation & Performance
 
-The data for Fig. 10 was generated using the `verification.py` script located in the [kda/scripts directory](https://github.com/Becksteinlab/kda/tree/master/kda/scripts) and saved here as `fig_10__kda_validation_and_performance/data.csv`. New data can be generated by following the instructions in the [README](https://github.com/Becksteinlab/kda/tree/master/kda/scripts#kda-verification).
+The data for **Figure 10** was generated using the `verification.py` script located in the [kda/scripts directory](https://github.com/Becksteinlab/kda/tree/master/kda/scripts) and saved here as `fig_10__kda_validation_and_performance/data.csv`. New data can be generated by following the instructions in the [README](https://github.com/Becksteinlab/kda/tree/master/kda/scripts#kda-verification).
 
 To generate the figures simply run the following from the `fig_10__kda_validation_and_performance` directory:
 
@@ -49,11 +49,11 @@ $ python make_6wl_plots.py
 This will create the following files:
 
 - `antiporter_data.csv`: Rate constants used for analysis
-- `6wl_analysis_data.csv`: Figure 11c raw data 
+- `6wl_analysis_data.csv`: Raw data (**Figure 11c**)
 - `tflux_data.csv`: Operational fluxes (calculated using net transition fluxes) raw data
-- `G_kinetic_diagram.*`: Kinetic diagram for the control model (Figure 11b)
-- `G_leak_kinetic_diagram.*`: Kinetic diagram for the leakage model (Figure 11b)
-- `6wl_analysis.*`: Fluxes vs. leakage rate panel figure (Figure 11c)
+- `G_kinetic_diagram.*`: Kinetic diagram for the control model (**Figure 11b**)
+- `G_leak_kinetic_diagram.*`: Kinetic diagram for the leakage model (**Figure 11b**)
+- `6wl_analysis.*`: Fluxes vs. leakage rate panel figure (**Figure 11c**)
 
 An additional file (`tflux_table_data.csv`) is included which was used to compare the raw data for the operational flux calculation method comparison in the paper (Section 3.3: Operational Fluxes in Terms of Net Transition Fluxes).
 
@@ -81,11 +81,11 @@ All generated figures can be found in either `main_analysis/plots/figures` or `m
 Here is a list of the key figures from the paper:
 
 - `emre_8_state_model.png`: kinetic diagram for the 8-state model of EmrE
-- `all_cycles.*`: All valid cycles for the 8-state model of EmrE (Figure 13)
-- `fig_7A.*`: Operational fluxes of EmrE for alternating access rate biasing (Figure 14a)
-- `fig_7B.*`: Operational fluxes of EmrE for substrate off-rate biasing (Figure 15a)
-- `fig_7A_flux_diagram_RAA_1E-08.*`, `fig_7A_flux_diagram_RAA_1E+00.*`, `fig_7A_flux_diagram_RAA_1E+08.*`: kinetic diagrams with transition-flux-weighted edges for alternating access rate biasing (Figures 14b-14d). The legends for each are included separately (i.e. `fig_7A_flux_diagram_RAA_1E+00_legend.*`).
-- `fig_7B_flux_diagram_kAA_1E+02_Roff_1E-10.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+00.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+02.*`: kinetic diagrams with transition-flux-weighted edges for substrate off-rate biasing (Figures 15b-15d). The legends for each are included separately.
+- `all_cycles.*`: All valid cycles for the 8-state model of EmrE (**Figure 13**)
+- `fig_7A.*`: Operational fluxes of EmrE for alternating access rate biasing (**Figure 14a**)
+- `fig_7B.*`: Operational fluxes of EmrE for substrate off-rate biasing (**Figure 15a**)
+- `fig_7A_flux_diagram_RAA_1E-08.*`, `fig_7A_flux_diagram_RAA_1E+00.*`, `fig_7A_flux_diagram_RAA_1E+08.*`: kinetic diagrams with transition-flux-weighted edges for alternating access rate biasing (**Figures 14b-14d**). The legends for each are included separately (i.e. `fig_7A_flux_diagram_RAA_1E+00_legend.*`).
+- `fig_7B_flux_diagram_kAA_1E+02_Roff_1E-10.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+00.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+02.*`: kinetic diagrams with transition-flux-weighted edges for substrate off-rate biasing (**Figures 15b-15d**). The legends for each are included separately.
 
 **NOTE:** `generate_figures.py` uses previously generated data (`main_analysis/data/all_figure_data.csv`) and sympy expressions (located in `main_analysis/fig_functions`) to speed up code execution. `all_figure_data.csv` can be re-generated using `generate_fig_data.py`. To generate new sympy expressions at run time, simply delete all files in the `main_analysis/fig_functions` directory and re-run `generate_figures.py`. 
 

kda_paper/fig_13-15__8_state_emre_model/main_analysis/README.md

@@ -22,10 +22,10 @@ All generated figures can be found in either `plots/figures` or `plots/flux_grap
 Here is a list of the key figures from the paper:
 
 - `emre_8_state_model.png`: kinetic diagram for the 8-state model of EmrE
-- `all_cycles.*`: All valid cycles for the 8-state model of EmrE (Figure 13)
-- `fig_7A.*`: Operational fluxes of EmrE for alternating access rate biasing (Figure 14a)
-- `fig_7B.*`: Operational fluxes of EmrE for substrate off-rate biasing (Figure 15a)
-- `fig_7A_flux_diagram_RAA_1E-08.*`, `fig_7A_flux_diagram_RAA_1E+00.*`, `fig_7A_flux_diagram_RAA_1E+08.*`: kinetic diagrams with transition-flux-weighted edges for alternating access rate biasing (Figures 14b-14d). The legends for each are included separately (i.e. `fig_7A_flux_diagram_RAA_1E+00_legend.*`).
-- `fig_7B_flux_diagram_kAA_1E+02_Roff_1E-10.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+00.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+02.*`: kinetic diagrams with transition-flux-weighted edges for substrate off-rate biasing (Figures 15b-15d). The legends for each are included separately.
+- `all_cycles.*`: All valid cycles for the 8-state model of EmrE (**Figure 13**)
+- `fig_7A.*`: Operational fluxes of EmrE for alternating access rate biasing (**Figure 14a**)
+- `fig_7B.*`: Operational fluxes of EmrE for substrate off-rate biasing (**Figure 15a**)
+- `fig_7A_flux_diagram_RAA_1E-08.*`, `fig_7A_flux_diagram_RAA_1E+00.*`, `fig_7A_flux_diagram_RAA_1E+08.*`: kinetic diagrams with transition-flux-weighted edges for alternating access rate biasing (**Figures 14b-14d**). The legends for each are included separately (i.e. `fig_7A_flux_diagram_RAA_1E+00_legend.*`).
+- `fig_7B_flux_diagram_kAA_1E+02_Roff_1E-10.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+00.*`, `fig_7B_flux_diagram_kAA_1E+02_Roff_1E+02.*`: kinetic diagrams with transition-flux-weighted edges for substrate off-rate biasing (**Figures 15b-15d**). The legends for each are included separately.
 
 **NOTE:** `generate_figures.py` uses previously generated data (`main_analysis/data/all_figure_data.csv`) and sympy expressions (located in `main_analysis/fig_functions`) to speed up code execution. `all_figure_data.csv` can be re-generated using `generate_fig_data.py`. To generate new sympy expressions at run time, simply delete all files in the `main_analysis/fig_functions` directory and re-run `generate_figures.py`.