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fix missing scaling values in label tables and fontsizes in fig5_s9 #58

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Merged
jcass11 merged 1 commit into from
Dec 10, 2024
Merged

fix missing scaling values in label tables and fontsizes in fig5_s9 #58

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3 changes: 2 additions & 1 deletion nuc_morph_analysis/analyses/volume/figure_5_s9_workflow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@
from nuc_morph_analysis.lib.visualization.plotting_tools import get_plot_labels_for_metric
from nuc_morph_analysis.lib.visualization.example_tracks import EXAMPLE_TRACKS

from nuc_morph_analysis.analyses.volume.plot_help import plot_dxdt_over_time_by_cell_cycle, adjust_axis_positions
from nuc_morph_analysis.analyses.volume.plot_help import plot_dxdt_over_time_by_cell_cycle, adjust_axis_positions, update_plotting_params
import matplotlib
import matplotlib.pyplot as plt

Expand Down Expand Up @@ -238,6 +238,7 @@

# %%
# S5 panel F and S9 panel E
update_plotting_params()
df_full = add_times.digitize_time_column(df_full,0,1,step_size=0.02,time_col='normalized_time',new_col='dig_time')
ycol = 'dxdt_48_volume'
colony_list = ['small','medium','large']
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67 changes: 11 additions & 56 deletions nuc_morph_analysis/lib/visualization/label_tables.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,65 +77,20 @@ def get_scale_factor_table(dataset="all_baseline"):
"2d_area_pseudo_cell",
): (pix_size/2.5)**2,
("2d_area_nuc_cell_ratio"): 1,
(
"dxdt_48_volume",
"neighbor_avg_dxdt_48_volume_whole_colony",
"neighbor_avg_dxdt_48_volume_90um",
"dxdt_t2-dxdt_t1",
): pix_size**3 / (time_interval_minutes / 60),
(
"dxdt_48_volume_dips_removed_um_unfilled",
"neighbor_avg_dxdt_48_volume_dips_removed_um_unfilled_90um",
"neighbor_avg_dxdt_48_volume_dips_removed_um_unfilled_whole_colony",
): 1 / (time_interval_minutes / 60),
}

# add a couple of dxdt columns
dict1.update({'dxdt_48_volume': 1/(time_interval_minutes/60)})
dict1.update({'dxdt_48_volume_dips_removed_um_unfilled': 1/(time_interval_minutes/60)})
dict1.update({'neighbor_avg_dxdt_48_volume_dips_removed_um_unfilled_90um': 1/(time_interval_minutes/60)})
dict1.update({'neighbor_avg_dxdt_48_volume_dips_removed_um_unfilled_whole_colony': 1/(time_interval_minutes/60)})



dict1.update({'dxdt_48_fit_volume_per_V': (1)/(time_interval_minutes/60)})

# add non dxdt columns and other non-traditional columns
hours_per_frame = time_interval_minutes / 60
temp_dict = get_one_to_one_dict(dict1)
for feature in DXDT_FEATURE_LIST:
dict1.update(
{
f"{DXDT_PREFIX}{bin_interval}_{feature}": temp_dict[feature] / (hours_per_frame)
for bin_interval in BIN_INTERVAL_LIST
}
)
dict1.update(
{
f"{DXDT_PREFIX}{bin_interval}_volume_per_V": 1 / (hours_per_frame)
for bin_interval in BIN_INTERVAL_LIST
}
)

for local_radius_str in LOCAL_RADIUS_STR_LIST:
for feature in NEIGHBOR_FEATURE_LIST:
dict1.update({f"{NEIGHBOR_PREFIX}{feature}_{local_radius_str}": temp_dict[feature]})
dict1.update(
{
f"{NEIGHBOR_PREFIX}{DXDT_PREFIX}{bin_interval}_{feature}_{local_radius_str}": temp_dict[
feature
]
/ (hours_per_frame)
for bin_interval in BIN_INTERVAL_LIST
}
)
# add {DXDT_PREFIX}{bin_interval}_volume_per_V
dict1.update(
{
f"{NEIGHBOR_PREFIX}{DXDT_PREFIX}{bin_interval}_volume_per_V_{local_radius_str}": 1
/ (hours_per_frame)
for bin_interval in BIN_INTERVAL_LIST
}
)

# add name for coordinated_local_growth_fig.py
for bin_interval in BIN_INTERVAL_LIST:
for local_radius_str in LOCAL_RADIUS_STR_LIST:
dict1.update({f"dxdt_t2-dxdt_t1": 1})
dict1.update({f"dvdt_t2-dvdt_t1_neighbors_{bin_interval}_{local_radius_str}": 1})
dict1.update({f"dvdt_t2-dvdt_t1_self_{bin_interval}_{local_radius_str}": 1})

# important for figure 5 supp: do NOT REMOVE
dict1.update({"dxdt_t2-dxdt_t1": temp_dict['volume'] / (hours_per_frame)})
return dict1


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