Python - plot module' object is not callable

Question

Fairly new to Python and receiving error: 'module' object is not callable.

Basically, I have a model with some reactions, I am using a for loop that changes some values of selected reactions and then I want to plot the output of the model as a function of the change in parameter. Perhaps my code will provide more of a concise answer, so here it is:

import cobra
import os
from os.path import join
import matplotlib.pyplot as plt

data_dir = '/Users/stephenchapman/Documents/research/FBA_algae_digesate/COBRApy/iCZ843/iCZ843_models'
model = cobra.io.read_sbml_model(join(data_dir, "iCZ843_mixo.xml"))
NH4_exchange = []
fluxes = []

for i in range(0,100,10):
    model.reactions[15].lower_bound = -i
    model.reactions[15].upper_bound = -i
    solution = model_mixo.optimize()    
    solution.f
    fluxes.append(solution.f)
    NH4_exchange.append(model.reactions[15].lower_bound)
plt('fluxes','NH4_exchange')
plt.show()

Can anyone please help me with this?

Cheers

S.

You probably mean plt.plot('fluxes','NH4_exchange') or something instead of plt('fluxes','NH4_exchange') — sacuL
– sacuL, Commented May 10, 2018 at 21:55
Hi Sacul, thanks for the reply, I see the difference: Did as suggested and received error: ValueError: Unrecognized character N in format string — Stephen Chapman
– Stephen Chapman, Commented May 10, 2018 at 22:05
Sounds like there is an issue with the data you're trying to plot (some element matplotlib doesn't know what to do with). Can't really help you unless you post a minimal reproducible example — sacuL
– sacuL, Commented May 10, 2018 at 22:08
just remove the quotes around fluxes and NH4_exchange. They are variables, not strings. — Jody Klymak
– Jody Klymak, Commented May 10, 2018 at 22:27

ImportanceOfBeingErnest · Accepted Answer · 2018-05-11 12:04:01Z

1

You want to plot arrays (or lists), not strings.

plt.plot(fluxes, NH4_exchange)

That being said, if you actually wanted to plot strings, they would need to have the same length and be converted to a list first, e.g.

plt.plot(list("fluxes"), list("change"))

would result in

answered May 11, 2018 at 12:04

ImportanceOfBeingErnest

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