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PEtab-dev / PEtab

PEtab - an SBML and TSV based data format for parameter estimation problems in systems biology
https://petab.readthedocs.io
MIT License
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Visualization: log yScale has no effect #197

Closed MerktSimon closed 4 years ago

MerktSimon commented 4 years ago

If you chose log or log10 in the field yScale in the visualization file it has no effect on the plot. Example Isensee: Figure_2

plotId plotName plotTypeSimulation plotTypeData datasetId xValues xOffset xLabel yValues yOffset yLabel legendEntry xScale yScale
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl fourABnOH_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy 4-ABnOH/Ctrl lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk fourABnOH_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy 4-ABnOH/Fsk(10) lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp_cAMPS_pAB_and_ctrl Rp_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp-cAMPS-pAB/Ctrl lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp_cAMPS_pAB_and_ctrl Rp_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp-cAMPS-pAB/Fsk(10) lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_ctrl Rp8_Br_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-Br-cAMPS-pAB/Ctrl lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk Rp8_Br_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-Br-cAMPS-pAB/Fsk(10) lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl Rp8_pCPT_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-pCPT-cAMPS-pAB/Ctrl lin lin
plot1 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_pCPT_cAMPS_pAB_and_Fsk Rp8_pCPT_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-pCPT-cAMPS-pAB/Fsk(10) lin lin
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_ctrl fourABnOH_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy 4-ABnOH/Ctrl lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__4_ABnOH_and_Fsk fourABnOH_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy 4-ABnOH/Fsk(10) lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp_cAMPS_pAB_and_ctrl Rp_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp-cAMPS-pAB/Ctrl lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp_cAMPS_pAB_and_ctrl Rp_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp-cAMPS-pAB/Fsk(10) lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_ctrl Rp8_Br_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-Br-cAMPS-pAB/Ctrl lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_Br_cAMPS_pAB_and_Fsk Rp8_Br_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-Br-cAMPS-pAB/Fsk(10) lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_pCPT_cAMPS_pAB_and_ctrl Rp8_pCPT_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-pCPT-cAMPS-pAB/Ctrl lin log
plot7 JI09_150302_Drg345_343_CycNuc LinePlot MeanAndSD JI09_150302_Drg345_343_CycNuc__Rp8_pCPT_cAMPS_pAB_and_Fsk Rp8_pCPT_cAMPS_pAB_incubation_time 0 Incubation Time [min] pRII_Microscopy 0 pRII_Microscopy Rp8-pCPT-cAMPS-pAB/Fsk(10) lin log
yannikschaelte commented 4 years ago

not sure if I understand the visualization folder correctly, but since "yScale" does not even appear in the whole folder except once when setting defaults, this is bound to not work.

in addition: also for xScale I assume log and log10 cannot give different results currently. In the implementation, one must use ax[axx, axy].set_xscale("log", basex=10) in plotting_config.py

MerktSimon commented 4 years ago

xScale is implemented actually. It can do "linear", "log(10)" and "order". Contrary to the data format documentation where "order" does not appear at all, there is no difference between "log" and "log10". The former does nothing and the latter results in the `set_xscale("log").

MerktSimon commented 4 years ago

we should agree on what log or log10 implies and which bases we want to use. Then I will implement this analogously for yscale

yannikschaelte commented 4 years ago

log would be to the basis e, and log10 for the basis 10, scaling the axis accordingly. those are the bases we allow for scaling in petab throughout.