@@ -38,7 +38,6 @@
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38 38
from cameo.strain_design.heuristic.evolutionary.processing import process_reaction_knockout_solution, \
39 39
    process_gene_knockout_solution, process_reaction_swap_solution
40 40
from cameo.util import TimeMachine
41 -
from cameo.visualization.plotting import plotter
42 41
from cameo.core.utils import get_reaction_for
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44 43
__all__ = ["OptGene"]
@@ -294,7 +293,7 @@
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            fluxes = self._simulation_method(self._model, **self._simulation_kwargs)
295 294
            fluxes.display_on_map(map_name=map_name, palette=palette)
296 295
297 -
    def plot(self, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
296 +
    def plot(self, plotter, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
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        wt_production = phenotypic_phase_plane(self._model, objective=self._target, variables=[self._biomass])
299 298
        with self._model:
300 299
            for ko in self.data_frame.loc[index, "reactions"]:
@@ -483,7 +482,7 @@
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            fluxes = self._simulation_method(self._model, **self._simulation_kwargs)
484 483
            fluxes.display_on_map(map_name=map_name, palette=palette)
485 484
486 -
    def plot(self, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
485 +
    def plot(self, plotter, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
487 486
        wt_production = phenotypic_phase_plane(self._model, objective=self._target, variables=[self._biomass])
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        with self._model:
489 488
            for ko in self.data_frame.loc[index, "reactions"]:

@@ -29,10 +29,9 @@
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29 29
from cobra.util import fix_objective_as_constraint, get_context
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from cobra.exceptions import OptimizationError
31 31
from numpy import trapz
32 -
from sympy import S
33 32
from optlang.interface import UNBOUNDED, OPTIMAL
33 +
from optlang.symbolics import Zero
34 34
35 -
import cameo
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from cameo import config
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from cameo.core.result import Result
38 37
from cameo.flux_analysis.util import remove_infeasible_cycles, fix_pfba_as_constraint
@@ -40,7 +39,6 @@
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from cameo.ui import notice
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from cameo.util import partition, _BIOMASS_RE_
42 41
from cameo.core.utils import get_reaction_for
43 -
from cameo.visualization.plotting import plotter
44 42
45 43
logger = logging.getLogger(__name__)
46 44
@@ -357,7 +355,7 @@
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357 355
    fva_sol = OrderedDict()
358 356
    lb_flags = dict()
359 357
    with model:
360 -
        model.objective = S.Zero
358 +
        model.objective = Zero
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        model.objective.direction = 'min'
363 361
        for reaction in reactions:
@@ -760,7 +758,7 @@
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760 758
    def data_frame(self):
761 759
        return pandas.DataFrame(self._phase_plane)
762 760
763 -
    def plot(self, grid=None, width=None, height=None, title=None, axis_font_size=None, palette=None,
761 +
    def plot(self, plotter, grid=None, width=None, height=None, title=None, axis_font_size=None, palette=None,
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             points=None, points_colors=None, estimate='flux', **kwargs):
765 763
        """plot phenotypic phase plane result
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@@ -882,7 +880,7 @@
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882 880
    def data_frame(self):
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        return self._data_frame
884 882
885 -
    def plot(self, index=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
883 +
    def plot(self, plotter, index=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
886 884
        if index is None:
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            index = self.data_frame.index[0:10]
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        fva_result = self.data_frame.loc[index]

@@ -23,7 +23,6 @@
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from cameo.core.result import Result
25 25
from cameo.core.target import EnsembleTarget, Target
26 -
from cameo.visualization.plotting import plotter
27 26
28 27
from gnomic import Genotype
29 28
@@ -180,7 +179,7 @@
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180 179
    def _repr_html_(self):
181 180
        return self.data_frame._repr_html_()
182 181
183 -
    def plot(self, grid=None, width=None, height=None, title=None, *args, **kwargs):
182 +
    def plot(self, plotter, grid=None, width=None, height=None, title=None, *args, **kwargs):
184 183
        if title is None:
185 184
            title = "Target frequency plot for %s result" % self.__method_name__
186 185

@@ -41,7 +41,6 @@
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from cameo.flux_analysis.simulation import fba
42 42
from cameo.flux_analysis.structural import find_coupled_reactions_nullspace
43 43
from cameo.util import reduce_reaction_set, decompose_reaction_groups
44 -
from cameo.visualization.plotting import plotter
45 44
46 45
logger = logging.getLogger(__name__)
47 46
@@ -385,7 +384,7 @@
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            fluxes = fba(self._model)
386 385
            fluxes.display_on_map(map_name=map_name, palette=palette)
387 386
388 -
    def plot(self, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
387 +
    def plot(self, plotter, index=0, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
389 388
        wt_production = phenotypic_phase_plane(self._model, objective=self._target, variables=[self._biomass.id])
390 389
        with self._model:
391 390
            for ko in self.data_frame.loc[index, "reactions"]:

@@ -37,7 +37,6 @@
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37 37
from cobra import Reaction, Metabolite
38 38
from cobra.util import fix_objective_as_constraint
39 39
40 -
from cameo.visualization.plotting import plotter
41 40
from cameo import config
42 41
43 42
from cameo.ui import notice
@@ -633,7 +632,7 @@
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633 632
        else:
634 633
            self._plot_production_envelope(title=title, grid=grid, width=width, height=height)
635 634
636 -
    def _plot_flux_variability_analysis(self, index, variables=None, title=None,
635 +
    def _plot_flux_variability_analysis(self, plotter, index, variables=None, title=None,
637 636
                                        width=None, height=None, palette=None, grid=None):
638 637
        if variables is None:
639 638
            variables = self.reference_fva.index[0:10]
@@ -1008,7 +1007,7 @@
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    __method_name__ = "FSEOF"
1010 1009
1011 -
    def plot(self, grid=None, width=None, height=None, title=None, *args, **kwargs):
1010 +
    def plot(self, plotter, grid=None, width=None, height=None, title=None, *args, **kwargs):
1012 1011
        if title is None:
1013 1012
            title = "FSEOF fluxes"
1014 1013

@@ -39,7 +39,6 @@
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39 39
from cameo.data import metanetx
40 40
from cameo.strain_design.pathway_prediction import util
41 41
from cameo.util import TimeMachine
42 -
from cameo.visualization.plotting import plotter
43 42
44 43
__all__ = ['PathwayPredictor']
45 44
@@ -172,7 +171,9 @@
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        # TODO: small pathway visualizations would be great.
173 172
        raise NotImplementedError
174 173
175 -
    def plot_production_envelopes(self, model, objective=None, title=None):
174 +
    def plot_production_envelopes(
175 +
        self, plotter, model, objective=None, title=None
176 +
    ):
176 177
        rows = int(ceil(len(self.pathways) / 2.0))
177 178
        title = "Production envelops for %s" % self.pathways[0].product.name if title is None else title
178 179
        grid = plotter.grid(n_rows=rows, title=title)
Files Coverage
cameo 62.46%
Project Totals (56 files) 62.46%
2433.2
3.6=.6
TRAVIS_OS_NAME=linux
2433.3
3.7=.7
TRAVIS_OS_NAME=linux

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