ode2tn 1.0.2__py3-none-any.whl → 1.0.3__py3-none-any.whl

ode2tn/transform.py

@@ -18,6 +18,7 @@ def plot_tn(
         scale: float = 1.0,
         t_span: tuple[float, float] | None = None,
         show_factors: bool = False,
+        latex_legend: bool = True,
         resets: dict[float, dict[sp.Symbol | str, float]] | None = None,
         dependent_symbols: dict[sp.Symbol | str, sp.Expr | str] | None = None,
         figure_size: tuple[float, float] = (10, 3),
@@ -61,6 +62,12 @@ def plot_tn(
             `symbols_to_plot` to ``[ratios, factors]``, where ratios is a list of dependent symbols
             `x=x_top/x_bot`, and factors is a list of symbols with the transcription factors `x_top`, `x_bot`,
             for each original variable `x`.
+        latex_legend: If True, surround each symbol name with dollar signs, unless it is already surrounded with them,
+            so that the legend is interpreted as LaTeX. If this is True, then the symbol name must either
+            start and end with `$`, or neither start nor end with `$`. Unlike in the gpac package, this is True
+            by default. The names of transcription factors are automatically surrounded by dollar signs.
+            This option makes sure the legend showing original variables (or dependent symbols) also have `$` added
+            so as to be interpreted as LaTeX.
         resets:
             If specified, this is a dict mapping times to "configurations"
             (i.e., dict mapping symbols/str to values).
@@ -112,6 +119,7 @@ def plot_tn(
         dependent_symbols=dependent_symbols_tn,
         resets=resets,
         figure_size=figure_size,
+        latex_legend=latex_legend,
         symbols_to_plot=symbols_to_plot,
         legend=legend,
         show=show,

{ode2tn-1.0.2.dist-info → ode2tn-1.0.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: ode2tn
-Version: 1.0.2
+Version: 1.0.3
 Summary: A Python package to turn arbitrary polynomial ODEs into a transcriptional network simulating it.
 Author-email: Dave Doty <doty@ucdavis.edu>
 License-Expression: MIT
@@ -14,7 +14,7 @@ Requires-Dist: scipy>=1.15
 Requires-Dist: sympy>=1.13
 Dynamic: license-file
 
-# ode-to-transcription-network
+# ode2tn
 ode2tn is a Python package to compile arbitrary polynomial ODEs into a transcriptional network simulating the ODEs.
 
 See this paper for details: TODO
@@ -52,31 +52,52 @@ inits = { # inits maps each symbol to its initial value
 }
 gamma = 2 # uniform decay constant; should be set sufficiently large that ???
 beta = 1 # constant introduced to keep values from going to infinity or 0
-t_eval = np.linspace(0, 6*pi, 1000)
-plot_tn(odes, inits, gamma=gamma, beta=beta, t_eval=t_eval, show_factors=True)
+tn_odes, tn_inits, tn_syms = ode2tn(odes, inits, gamma=gamma, beta=beta)
+gp.display_odes(tn_odes)
+print(f'{tn_inits=}')
+print(f'{tn_syms=}')
 ```
 
-This will print
+When run in a Jupyter notebook, this will show
+
+![](ode-display.png)
+
+showing that the variables `x` and `y` have been replace by pairs `x_t,x_b` and `y_t,y_b`, whose ratios `x_t/x_b` and `y_t/y_b` will track the values of the original variable `x` and `y` over time.
 
+If not in a Jupyter notebook, one could also inspect the transcriptional network ODEs via
+```python
+for var, ode in tn_odes.items():
+    print(f"{var}' = {ode}")
+```
+which would print a text-based version of the equations:
 ```
 x_t' = x_b*y_t/y_b - 2*x_t + x_t/x_b
 x_b' = 2*x_b**2/x_t - 2*x_b + 1
 y_t' = 2*y_b - 2*y_t + y_t/y_b
 y_b' = -2*y_b + 1 + x_t*y_b**2/(x_b*y_t)
-tn_inits={x_t: 2, x_b: 1, y_t: 1, y_b: 1}
-tn_syms={x: (x_t, x_b), y: (y_t, y_b)}
 ```
 
-showing that the variables `x` and `y` have been replace by pairs `x_t,x_b` and `y_t,y_b`, whose ratios `x_t/x_b` and `y_t/y_b` will track the values of the original variable `x` and `y` over time.
-The function `plot_tn` above does this conversion and then plots the ratios.
-Running the code above in a Jupyter notebook will print the above text and show this figure:
+The function `plot_tn` above does this conversion on the *original* odes and then plots the ratios.
+Running 
+
+```python
+t_eval = np.linspace(0, 6*pi, 1000)
+# note below it is odes and inits, not tn_odes and tn_inits
+# plot_tn calls ode2tn to convert the ODEs before plotting
+plot_tn(odes, inits, gamma=gamma, beta=beta, t_eval=t_eval, show_factors=True)
+```
+
+in a Jupyter notebook will show this figure:
 
 ![](sine-cosine-plot.svg)
 
-One could also hand the transcriptional network ODEs to gpac to integrate, if you want to directly access the data being plotted above.
+The parameter `show_factors` above indicates to show a second subplot with the underlying transcription factors ($x^\top, x^\bot, y^\top, y^\bot$ above).
+If left unspecified, it defaults to `False` and plots only the original values (ratios of pairs of transcription factors, $x,y$ above).
+
+One could also hand the transcriptional network ODEs to [gpac](https://github.com/UC-Davis-molecular-computing/gpac) to integrate, if you want to directly access the data being plotted above.
 The `OdeResult` object returned by `gpac.integrate_odes` is the same returned by [`scipy.integrate.solve_ivp`](https://docs.scipy.org/doc/scipy/reference/generated/scipy.integrate.solve_ivp.html), where the return value `sol` has a field `sol.y` that has the values of the variables in the order they were inserted into `tn_odes`, which will be the same as the order in which the original variables `x` and `y` were inserted, with `x_t` coming before `x_b`:
 
-```
+```python
 t_eval = np.linspace(0, 2*pi, 5)
 sol = gp.integrate_odes(tn_odes, tn_inits, t_eval)
 print(f'times = {sol.t}')

ode2tn-1.0.3.dist-info/RECORD

@@ -0,0 +1,7 @@
+ode2tn/__init__.py,sha256=b_mINIsNfCWzgG7QVYMsRsWKDLvp2QKFAzRqWtYqwDA,30
+ode2tn/transform.py,sha256=8GciVR2iGRRWgKyvPoYoQ5TZjKrOdNyzaH_ZukJiVsw,16829
+ode2tn-1.0.3.dist-info/licenses/LICENSE,sha256=VV9UH0kkG-2edZvwJOqgtN12bZIzs2vn9_cq1SjoUJc,1091
+ode2tn-1.0.3.dist-info/METADATA,sha256=RbwHIvSA6PgVWV9I57Fs9n2OdU7ocksS65YPaxs7174,4882
+ode2tn-1.0.3.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
+ode2tn-1.0.3.dist-info/top_level.txt,sha256=fPQ9s5yLIYfazJS7wBBfU9EsWa9RGALq8VL-wUYRlao,7
+ode2tn-1.0.3.dist-info/RECORD,,

ode2tn-1.0.2.dist-info/RECORD

@@ -1,7 +0,0 @@
-ode2tn/__init__.py,sha256=b_mINIsNfCWzgG7QVYMsRsWKDLvp2QKFAzRqWtYqwDA,30
-ode2tn/transform.py,sha256=8gQVHaCRTdiACQPZdkB3OPfc2KOZTA3YwMgbXDDnNkE,16155
-ode2tn-1.0.2.dist-info/licenses/LICENSE,sha256=VV9UH0kkG-2edZvwJOqgtN12bZIzs2vn9_cq1SjoUJc,1091
-ode2tn-1.0.2.dist-info/METADATA,sha256=MSGeKttEB-ImlNvBof07AeyxR1rOCBf48tUNinaIgS0,4095
-ode2tn-1.0.2.dist-info/WHEEL,sha256=pxyMxgL8-pra_rKaQ4drOZAegBVuX-G_4nRHjjgWbmo,91
-ode2tn-1.0.2.dist-info/top_level.txt,sha256=fPQ9s5yLIYfazJS7wBBfU9EsWa9RGALq8VL-wUYRlao,7
-ode2tn-1.0.2.dist-info/RECORD,,