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Sneyd: prettify visualization #310
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18 changes: 9 additions & 9 deletions
18
Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,10 @@ | ||
| plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale datasetId legendEntry yValues xValues xOffset yOffset | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__1_open_probability 10 μM IP_3, 0.1 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP_3, 0.2 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP_3, 1 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP_3, 3 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP_3, 10 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP_3, 0.4 μM $Ca^{2+}$ - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__1_open_probability 10 μM IP$_3$, 0.1 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP$_3$, 0.2 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP$_3$, 1 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP$_3$, 3 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP$_3$, 10 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
18 changes: 9 additions & 9 deletions
18
Benchmark-Models/Sneyd_PNAS2002/visualizationSpecification_Sneyd_PNAS2002_subplots.tsv
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,10 +1,10 @@ | ||
| plotId plotTypeData plotName plotTypeSimulation xLabel xScale yLabel yScale datasetId legendEntry yValues xValues xOffset yOffset | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__1_open_probability 10 μM IP_3, 0.1 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP_3, 0.2 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot3 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot4 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP_3, 1 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot5 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP_3, 3 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot6 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP_3, 10 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot7 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot8 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot9 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP_3, 0.4 μM Ca^{2+} - open_probability open_probability time 0 0 | ||
| plot1 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__1_open_probability 10 μM IP$_3$, 0.1 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot2 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__2_open_probability 10 μM IP$_3$, 0.2 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot3 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__3_open_probability 10 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot4 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__4_open_probability 10 μM IP$_3$, 1 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot5 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__5_open_probability 10 μM IP$_3$, 3 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot6 MeanAndSD LinePlot time [s] lin open probability lin Ca_dose_response__6_open_probability 10 μM IP$_3$, 10 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot7 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__1_open_probability 3 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot8 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__2_open_probability 5 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 | ||
| plot9 MeanAndSD LinePlot time [s] lin open probability lin IP3_dose_response__3_open_probability 10 μM IP$_3$, 0.4 μM Ca$^{2{+}}$ open_probability time 0 0 |
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Is there an issue with using
$Ca^{2+}$?There was a problem hiding this comment.
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Yes,
Cashouldn't be italicized.Uh oh!
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One could set
matplotlib.rcParams["mathtext.default"] = "regular", right? (As a default in the visualization module)But that wouldn't be good when displaying actual equations - So I think that's a good way to solve the issue.
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Good point, but with using
Ca$^{2+}$?Uh oh!
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I think no issue... last time I tried it rendered correctly - not sure whether I had to set some
matplotlib.rcParamsadditionally or not, but I believe no. Just less legible IMHO.There was a problem hiding this comment.
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Sure, that works as well.
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Related:
\mathrmalso works it seems, i.e.$\\mathrm{Ca}^{2+}$There was a problem hiding this comment.
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Yup. When I was asked to look at the visualization, I did not consider this due to legibility.