add shared time markers to phase portraits (pinellolab#359)

* compare t0 and maximum shared time; add u0/s0/uinf/sinf in phase portraits
* update lock file

---------

Co-authored-by: Cameron Smith <cameron.ray.smith@gmail.com>

pyrovelocity/config.py

@@ -525,6 +525,7 @@ def create_reports_config(model_name: str, model_number: int):
             uncertainty_param_plot=f"{path}/param_uncertainties.pdf",
             vector_field_plot=f"{path}/vector_field.pdf",
             posterior_phase_portraits=f"{path}/posterior_phase_portraits",
+            t0_selection=f"{path}/t0_selection.tif",
             biomarker_selection_plot=f"{path}/markers_selection_scatterplot.tif",
             biomarker_phaseportrait_plot=f"{path}/markers_phaseportrait.pdf",
             fig2_part1_plot=f"{path}/fig2_part1_plot.pdf",

reproducibility/figures/config.yaml

@@ -699,6 +699,7 @@ reports:
       uncertainty_param_plot: reports/pancreas_model2/param_uncertainties.pdf
       vector_field_plot: reports/pancreas_model2/vector_field.pdf
       posterior_phase_portraits: reports/pancreas_model2/posterior_phase_portraits
+      t0_selection: reports/pancreas_model2/t0_selection.tif
       biomarker_selection_plot: reports/pancreas_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pancreas_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pancreas_model2/fig2_part1_plot.pdf
@@ -716,6 +717,7 @@ reports:
       uncertainty_param_plot: reports/bonemarrow_model2/param_uncertainties.pdf
       vector_field_plot: reports/bonemarrow_model2/vector_field.pdf
       posterior_phase_portraits: reports/bonemarrow_model2/posterior_phase_portraits
+      t0_selection: reports/bonemarrow_model2/t0_selection.tif
       biomarker_selection_plot: reports/bonemarrow_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/bonemarrow_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/bonemarrow_model2/fig2_part1_plot.pdf
@@ -733,6 +735,7 @@ reports:
       uncertainty_param_plot: reports/pbmc68k_model2/param_uncertainties.pdf
       vector_field_plot: reports/pbmc68k_model2/vector_field.pdf
       posterior_phase_portraits: reports/pbmc68k_model2/posterior_phase_portraits
+      t0_selection: reports/pbmc68k_model2/t0_selection.tif
       biomarker_selection_plot: reports/pbmc68k_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pbmc68k_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pbmc68k_model2/fig2_part1_plot.pdf
@@ -750,6 +753,7 @@ reports:
       uncertainty_param_plot: reports/pons_model2/param_uncertainties.pdf
       vector_field_plot: reports/pons_model2/vector_field.pdf
       posterior_phase_portraits: reports/pons_model2/posterior_phase_portraits
+      t0_selection: reports/pons_model2/t0_selection.tif
       biomarker_selection_plot: reports/pons_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pons_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pons_model2/fig2_part1_plot.pdf
@@ -767,6 +771,7 @@ reports:
       uncertainty_param_plot: reports/pbmc10k_model2/param_uncertainties.pdf
       vector_field_plot: reports/pbmc10k_model2/vector_field.pdf
       posterior_phase_portraits: reports/pbmc10k_model2/posterior_phase_portraits
+      t0_selection: reports/pbmc10k_model2/t0_selection.tif
       biomarker_selection_plot: reports/pbmc10k_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pbmc10k_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pbmc10k_model2/fig2_part1_plot.pdf
@@ -784,6 +789,7 @@ reports:
       uncertainty_param_plot: reports/pbmc5k_model2/param_uncertainties.pdf
       vector_field_plot: reports/pbmc5k_model2/vector_field.pdf
       posterior_phase_portraits: reports/pbmc5k_model2/posterior_phase_portraits
+      t0_selection: reports/pbmc5k_model2/t0_selection.tif
       biomarker_selection_plot: reports/pbmc5k_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/pbmc5k_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/pbmc5k_model2/fig2_part1_plot.pdf
@@ -801,6 +807,7 @@ reports:
       uncertainty_param_plot: reports/larry_tips_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_tips_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_tips_model2/posterior_phase_portraits
+      t0_selection: reports/larry_tips_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_tips_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_tips_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_tips_model2/fig2_part1_plot.pdf
@@ -818,6 +825,7 @@ reports:
       uncertainty_param_plot: reports/larry_mono_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_mono_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_mono_model2/posterior_phase_portraits
+      t0_selection: reports/larry_mono_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_mono_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_mono_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_mono_model2/fig2_part1_plot.pdf
@@ -835,6 +843,7 @@ reports:
       uncertainty_param_plot: reports/larry_neu_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_neu_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_neu_model2/posterior_phase_portraits
+      t0_selection: reports/larry_neu_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_neu_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_neu_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_neu_model2/fig2_part1_plot.pdf
@@ -852,6 +861,7 @@ reports:
       uncertainty_param_plot: reports/larry_multilineage_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_multilineage_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_multilineage_model2/posterior_phase_portraits
+      t0_selection: reports/larry_multilineage_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_multilineage_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_multilineage_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_multilineage_model2/fig2_part1_plot.pdf
@@ -869,6 +879,7 @@ reports:
       uncertainty_param_plot: reports/larry_model2/param_uncertainties.pdf
       vector_field_plot: reports/larry_model2/vector_field.pdf
       posterior_phase_portraits: reports/larry_model2/posterior_phase_portraits
+      t0_selection: reports/larry_model2/t0_selection.tif
       biomarker_selection_plot: reports/larry_model2/markers_selection_scatterplot.tif
       biomarker_phaseportrait_plot: reports/larry_model2/markers_phaseportrait.pdf
       fig2_part1_plot: reports/larry_model2/fig2_part1_plot.pdf