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add shared time markers to phase portraits #359

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merged 5 commits into from
Jun 30, 2023
+305 −168
Merged

add shared time markers to phase portraits #359

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f216d30
dvc repro
qinqian Jun 24, 2023
c062e96
compare t0 and maximum shared time; add u0/s0/uinf/sinf in phase port…
qinqian Jun 24, 2023
fc65515
update dvc.lock
qinqian Jun 24, 2023
6ddc8f8
lint summarize
cameronraysmith Jun 30, 2023
049e69d
update lock file
cameronraysmith Jun 30, 2023
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1 change: 1 addition & 0 deletions pyrovelocity/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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",
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11 changes: 11 additions & 0 deletions reproducibility/figures/config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand All @@ -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
Expand Down
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