def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
# Get time
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time")
# Get tRNA IDs and counts
sim_data = cPickle.load(open(simDataFile, "rb"))
isTRna = sim_data.process.transcription.rnaData["isTRna"]
rnaIds = sim_data.process.transcription.rnaData["id"][isTRna]
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnaIndexes = np.array(
[moleculeIds.index(moleculeId) for moleculeId in rnaIds], np.int)
rnaCountsBulk = bulkMolecules.readColumn("counts")[:, rnaIndexes]
bulkMolecules.close()
# Plot
fig = plt.figure(figsize=(8.5, 11))
ax = plt.subplot(1, 1, 1)
ax.plot(time, rnaCountsBulk)
ax.set_xlim([time[0], time[-1]])
ax.set_xlabel("Time (s)")
ax.set_ylabel("Counts of tRNAs")
ax.spines["right"].set_visible(False)
ax.spines["top"].set_visible(False)
ax.tick_params(right="off", top="off", which="both", direction="out")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
rnaIds = [
"EG10367_RNA[c]",
"EG11036_RNA[c]",
"EG50002_RNA[c]",
"EG10671_RNA[c]",
"EG50003_RNA[c]",
"EG10669_RNA[c]",
"EG10873_RNA[c]",
"EG12179_RNA[c]",
"EG10321_RNA[c]",
"EG10544_RNA[c]",
]
names = [
"gapA - Glyceraldehyde 3-phosphate dehydrogenase",
"tufA - Elongation factor Tu",
"rpmA - 50S Ribosomal subunit protein L27",
"ompF - Outer membrane protein F",
"acpP - Apo-[acyl carrier protein]",
"ompA - Outer membrane protein A",
"rplL - 50S Ribosomal subunit protein L7/L12 dimer",
"cspE - Transcription antiterminator and regulator of RNA stability",
"fliC - Flagellin",
"lpp - Murein lipoprotein",
]
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnaIndexes = np.array([moleculeIds.index(x) for x in rnaIds], np.int)
rnaCounts = bulkMolecules.readColumn("counts")[:, rnaIndexes]
bulkMolecules.close()
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
plt.figure(figsize=(8.5, 11))
for subplotIdx in xrange(1, 10):
plt.subplot(3, 3, subplotIdx)
plt.plot(time / 60., rnaCounts[:, subplotIdx])
plt.xlabel("Time (min)")
plt.ylabel("mRNA counts")
plt.title(names[subplotIdx].split(" - ")[0])
plt.subplots_adjust(hspace=0.5, top=0.95, bottom=0.05)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, "seedOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
fig = plt.figure()
v = venn3(subsets=dataArea,
set_labels=["0 < Freq. < 1", "Freq. = 1", "Freq. = 0"])
ids = ["100", "010", "001", "110", "101", "011", "111"]
for i, color in zip(
ids, ["b", "r", "y", "purple", "green", "orange", "white"]):
v.get_patch_by_id(i).set_color(color)
for label, color in zip(v.set_labels, ["b", "r", "y"]):
label.set_color(color)
v.get_label_by_id("011").set_text("%s" % data[-2])
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
for i in ids:
v.get_label_by_id(i).set_text("")
for label in v.set_labels:
label.set_text("")
plt.savefig(os.path.join(plotOutDir, plotOutFileName + "__clean.pdf"))
plt.close()
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
waterIndex = np.array(moleculeIds.index('WATER[c]'), np.int)
waterCount = bulkMolecules.readColumn("counts")[:, waterIndex]
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
bulkMolecules.close()
plt.figure(figsize=(8.5, 11))
plt.plot(time / 60., waterCount, linewidth=2)
plt.xlabel("Time (min)")
plt.ylabel("WATER[c] counts")
plt.title("Counts of water")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
ribosomeData = TableReader(os.path.join(simOutDir, "RibosomeData"))
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
fractionStalled = ribosomeData.readColumn("fractionStalled")
ribosomeData.close()
plt.figure(figsize=(8.5, 11))
plt.plot(time / 60, fractionStalled)
plt.xlabel("Time (min)")
plt.ylabel("Fraction of ribosomes stalled")
plt.subplots_adjust(hspace=0.5, wspace=0.5)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, "seedOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
ap = AnalysisPaths(seedOutDir, multi_gen_plot=True)
# Get all cells
allDir = ap.get_cells()
cellCycleLengths = []
generations = []
for idx, simDir in enumerate(allDir):
simOutDir = os.path.join(simDir, "simOut")
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir,
"Main")).readColumn("time")
cellCycleLengths.append((time[-1] - time[0]) / 60. / 60.)
generations.append(idx)
plt.scatter(generations, cellCycleLengths)
plt.xlabel('Generation')
plt.ylabel('Time (hr)')
plt.title('Cell cycle lengths')
plt.xticks(generations)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, inputDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if metadata is not None and SHUFFLE_VARIANT_TAG not in metadata[
"variant"]:
print "This plot only runs for variants where parameters are shuffled."
return
if not os.path.isdir(inputDir):
raise Exception, "variantDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
validation_data = cPickle.load(open(validationDataFile, "rb"))
schmidtCounts = validation_data.protein.schmidt2015Data[
"glucoseCounts"]
ap = AnalysisPaths(inputDir, variant_plot=True)
pool = Pool(processes=parallelization.plotter_cpus())
args = zip(
range(ap.n_variant), [ap] * ap.n_variant,
[validation_data.protein.schmidt2015Data["monomerId"].tolist()] *
ap.n_variant, [schmidtCounts] * ap.n_variant)
result = pool.map(getPCC, args)
# cPickle.dump(result, open("pcc_results.cPickle", "w"), cPickle.HIGHEST_PROTOCOL)
pool.close()
pool.join()
# result = cPickle.load(open("pcc_results.cPickle", "r"))
controlPcc, controlPvalue = result[0]
pccs, pvals = zip(*result[1:])
pccs = np.array(pccs)
pvals = np.array(pvals)
fig = plt.figure()
fig.set_figwidth(5)
fig.set_figheight(5)
ax = plt.subplot(1, 1, 1)
pccs = np.array([x for x in pccs if not np.isnan(x)])
ax.hist(pccs, np.sqrt(pccs.size))
ax.axvline(controlPcc, color="k", linestyle="dashed", linewidth=2)
ax.set_xlabel("Proteome correlation (Pearson r)")
ax.set_title("Mean: %0.3g Std: %0.3g Control: %0.3g" %
(pccs.mean(), pccs.std(), controlPcc))
axes_list = [ax]
for a in axes_list:
for tick in a.yaxis.get_major_ticks():
tick.label.set_fontsize(FONT_SIZE)
for tick in a.xaxis.get_major_ticks():
tick.label.set_fontsize(FONT_SIZE)
whitePadSparklineAxis(ax)
plt.subplots_adjust(bottom=0.2, wspace=0.3)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
rnaIds = [
"EG10789_RNA[c]",
"EG11556_RNA[c]",
"EG12095_RNA[c]",
"G1_RNA[c]",
"G360_RNA[c]",
"EG10944_RNA[c]",
"EG12419_RNA[c]",
"EG10372_RNA[c]",
"EG10104_RNA[c]",
"EG10539_RNA[c]",
]
names = [
"ptsI - PTS enzyme I",
"talB - Transaldolase",
"secG - SecG",
"thiS - ThiS protein",
"flgD - Flagellar biosynthesis",
"serA - (S)-2-hydroxyglutarate reductase",
"gatY - GatY",
"gdhA - Glutamate dehydrogenase",
"atpG - ATP synthase F1 complex - gamma subunit",
"livJ - Branched chain amino acid ABC transporter - periplasmic binding protein",
]
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnaIndexes = np.array([moleculeIds.index(x) for x in rnaIds], np.int)
rnaCounts = bulkMolecules.readColumn("counts")[:, rnaIndexes]
bulkMolecules.close()
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
plt.figure(figsize=(8.5, 11))
for subplotIdx in xrange(1, 10):
plt.subplot(3, 3, subplotIdx)
plt.plot(time / 60., rnaCounts[:, subplotIdx])
plt.xlabel("Time (min)")
plt.ylabel("mRNA counts")
plt.title(names[subplotIdx].split(" - ")[0])
plt.subplots_adjust(hspace=0.5, top=0.95, bottom=0.05)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
rnaIds = [
"G7355_RNA[c]",
"EG11783_RNA[c]",
"G7742_RNA[c]",
"G6253_RNA[c]",
"EG10632_RNA[c]",
"EG11484_RNA[c]",
"G7889_RNA[c]",
"EG10997_RNA[c]",
"EG10780_RNA[c]",
"EG11060_RNA[c]",
]
names = [
"ypjD - Predicted inner membrane protein",
"intA - CP4-57 prophage; integrase",
"yrfG - Purine nucleotidase",
"ylaC - Predicted inner membrane protein",
"nagA - N-acetylglucosamine-6-phosphate deacetylase",
"yigZ - Predicted elongation factor",
"lptG - LptG (part of LPS transport system)",
"mnmE - GTPase, involved in modification of U34 in tRNA",
"pspE - Thiosulfate sulfurtransferase",
"ushA - UDP-sugar hydrolase / 5'-ribonucleotidase / 5'-deoxyribonucleotidase",
]
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnaIndexes = np.array([moleculeIds.index(x) for x in rnaIds], np.int)
rnaCounts = bulkMolecules.readColumn("counts")[:, rnaIndexes]
bulkMolecules.close()
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
plt.figure(figsize=(8.5, 11))
for subplotIdx in xrange(1, 10):
plt.subplot(3, 3, subplotIdx)
plt.plot(time / 60., rnaCounts[:, subplotIdx])
plt.xlabel("Time (min)")
plt.ylabel("mRNA counts")
plt.title(names[subplotIdx].split(" - ")[0])
plt.subplots_adjust(hspace=0.5, top=0.95, bottom=0.05)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, 'seedOutDir does not currently exist as a directory'
filepath.makedirs(plotOutDir)
with open(simDataFile, 'rb') as f:
sim_data = cPickle.load(f)
with open(validationDataFile, 'rb') as f:
validation_data = cPickle.load(f)
ap = AnalysisPaths(seedOutDir, multi_gen_plot=True)
for sim_dir in ap.get_cells():
simOutDir = os.path.join(sim_dir, 'simOut')
# Listeners used
main_reader = TableReader(os.path.join(simOutDir, 'Main'))
# Load data
time = main_reader.readColumn('time')
plt.figure()
### Create Plot ###
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close('all')
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, "seedOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
ap = AnalysisPaths(seedOutDir, multi_gen_plot = True)
# TODO: Declutter Y-axis
# Get first cell from each generation
firstCellLineage = []
for gen_idx in range(ap.n_generation):
firstCellLineage.append(ap.get_cells(generation = [gen_idx])[0])
massNames = [
#"dryMass",
"proteinMass",
"tRnaMass",
"rRnaMass",
'mRnaMass',
"dnaMass"
]
cleanNames = [
#"Dry\nmass",
"Protein\nmass frac.",
"tRNA\nmass frac.",
"rRNA\nmass frac.",
"mRNA\nmass frac.",
"DNA\nmass frac."
]
fig, axesList = plt.subplots(len(massNames), sharex = True)
for simDir in firstCellLineage:
simOutDir = os.path.join(simDir, "simOut")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time")
mass = TableReader(os.path.join(simOutDir, "Mass"))
massData = np.zeros((len(massNames),time.size))
for idx, massType in enumerate(massNames):
massData[idx,:] = mass.readColumn(massNames[idx])
massData = massData / massData.sum(axis = 0)
for idx, massType in enumerate(massNames):
axesList[idx].plot(time / 60, massData[idx,:])
axesList[idx].set_ylabel(cleanNames[idx])
for axes in axesList:
axes.set_yticks(list(axes.get_ylim()))
axesList[-1].set_xlabel('Time (min)')
exportFigure(plt, plotOutDir, plotOutFileName,metadata)
plt.close("all")
def do_plot(self, variantDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(variantDir):
raise Exception, "variantDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
# Get all cells in each seed
ap = AnalysisPaths(variantDir, cohort_plot=True)
max_cells_in_gen = 0
for genIdx in range(ap.n_generation):
n_cells = len(ap.get_cells(generation=[genIdx]))
if n_cells > max_cells_in_gen:
max_cells_in_gen = n_cells
fig, axesList = plt.subplots(ap.n_generation, sharex=True)
doubling_time = np.zeros((max_cells_in_gen, ap.n_generation))
for genIdx in range(ap.n_generation):
gen_cells = ap.get_cells(generation=[genIdx])
for simDir in gen_cells:
simOutDir = os.path.join(simDir, "simOut")
time = TableReader(os.path.join(simOutDir,
"Main")).readColumn("time")
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
doubling_time[np.where(simDir == gen_cells)[0],
genIdx] = (time.max() - initialTime) / 60.
# Plot initial vs final masses
if ap.n_generation == 1:
axesList = [axesList]
for idx, axes in enumerate(axesList):
if max_cells_in_gen > 1:
axes.hist(doubling_time[:, idx].flatten(),
int(np.ceil(np.sqrt(doubling_time[:, idx].size))))
else:
axes.plot(doubling_time[:, idx], 1, 'x')
axes.set_ylim([0, 2])
axes.axvline(doubling_time[:, idx].mean(),
color='k',
linestyle='dashed',
linewidth=2)
axes.text(
doubling_time[:, idx].mean(), 1, "Mean: %.3f Var: %.3f" %
(doubling_time[:, idx].mean(), doubling_time[:, idx].var()))
axesList[-1].set_xlabel("Doubling time (min))")
axesList[ap.n_generation / 2].set_ylabel("Frequency")
plt.subplots_adjust(hspace=0.2, wspace=0.5)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
sim_data = cPickle.load(open(simDataFile, "rb"))
isMRna = sim_data.process.transcription.rnaData["isMRna"]
isRRna = sim_data.process.transcription.rnaData["isRRna"]
isTRna = sim_data.process.transcription.rnaData["isTRna"]
rnaSynthProbListener = TableReader(os.path.join(simOutDir, "RnaSynthProb"))
rnaIds = rnaSynthProbListener.readAttribute('rnaIds')
rnaSynthProb = rnaSynthProbListener.readColumn('rnaSynthProb')
time = rnaSynthProbListener.readColumn('time')
rnaSynthProbListener.close()
mRnaSynthProb = rnaSynthProb[:, isMRna].sum(axis = 1)
rRnaSynthProb = rnaSynthProb[:, isRRna].sum(axis = 1)
tRnaSynthProb = rnaSynthProb[:, isTRna].sum(axis = 1)
# Plot
rows = 3
cols = 1
fig = plt.figure(figsize = (11, 8.5))
plt.figtext(0.4, 0.96, "RNA synthesis probabilities over time", fontsize = 12)
nMRnas = np.sum(isMRna)
nRRnas = np.sum(isRRna)
nTRnas = np.sum(isTRna)
subplotOrder = [mRnaSynthProb, rRnaSynthProb, tRnaSynthProb]
subplotTitles = ["mRNA\n(sum of %s mRNAs)" % nMRnas, "rRNA\n(sum of %s rRNAs)" % nRRnas, "tRNA\n(sum of %s tRNAs)" % nTRnas]
for index, rnaSynthProb in enumerate(subplotOrder):
ax = plt.subplot(rows, cols, index + 1)
ax.plot(time, rnaSynthProb)
ax.set_title(subplotTitles[index], fontsize = 10)
ymin = np.min(rnaSynthProb)
ymax = np.max(rnaSynthProb)
yaxisBuffer = np.around(1.2*(ymax - ymin), 3)
ax.set_ylim([ymin, yaxisBuffer])
ax.set_yticks([ymin, ymax, yaxisBuffer])
ax.set_yticklabels([ymin, np.around(ymax, 3), yaxisBuffer], fontsize = 10)
ax.set_xlim([time[0], time[-1]])
ax.tick_params(axis = "x", labelsize = 10)
ax.spines["left"].set_visible(False)
ax.spines["right"].set_visible(False)
plt.subplots_adjust(hspace = 0.5, )
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
sim_data = cPickle.load(open(simDataFile))
# Get exchange flux data
fbaResults = TableReader(os.path.join(simOutDir, "FBAResults"))
initialTime = units.s * TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = units.s * TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
externalExchangeFluxes = fbaResults.readColumn("externalExchangeFluxes")
externalMoleculeIDs = np.array(fbaResults.readAttribute("externalMoleculeIDs"))
fbaResults.close()
massExchange = sim_data.getter.getMass(externalMoleculeIDs).asNumber(units.g / units.mmol) * externalExchangeFluxes # g / gDCW-hr
# Get growth rate data
growthRateData = TableReader(os.path.join(simOutDir, "Mass"))
growthRate = ((1 / units.s) * growthRateData.readColumn("instantaniousGrowthRate")).asUnit(1 / units.h) # g / gDCW-hr
doublingTime = (1 / growthRate) * np.log(2)
# Plot stuff
fig = plt.figure()
fig.set_size_inches(8.5,11)
ax1 = plt.subplot(3,1,1)
ax1.plot(time.asNumber(units.min), doublingTime.asNumber(units.min))
ax1.plot(time.asNumber(units.min), sim_data.doubling_time.asNumber(units.min) * np.ones(time.asNumber().size), linestyle='--')
medianDoublingTime = np.median(doublingTime.asNumber(units.min)[1:])
ax1.set_ylim([medianDoublingTime - 2*medianDoublingTime, medianDoublingTime + 2*medianDoublingTime])
ax1.set_ylabel("Doubling\ntime (min)")
ax2 = plt.subplot(3,1,2)
ax2.plot(time.asNumber(units.min), massExchange)
maxMassExchange = massExchange[100:].max()
minMassExchange = massExchange[100:].min()
ax2.set_ylim([minMassExchange, maxMassExchange])
ax2.set_ylabel("Mass exchange\n(g / gDCW-hr)")
ax3 = plt.subplot(3,1,3)
water = massExchange[:, np.where(externalMoleculeIDs == "WATER[p]")[0][0]].copy()
waterAll = massExchange[:, np.where(externalMoleculeIDs == "WATER[p]")[0][0]].copy()
water[doublingTime.asNumber() > 0.] = np.nan
ax3.plot(time.asNumber(units.min), waterAll, 'k.')
ax3.plot(time.asNumber(units.min), water, 'b.')
maxMassExchange = massExchange[100:].max()
minMassExchange = massExchange[100:].min()
ax3.set_ylim([minMassExchange, maxMassExchange])
ax3.set_ylabel("Water exchange\nwhen doubling time < 0")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
# Get the names of rnas from the KB
sim_data = cPickle.load(open(simDataFile, "rb"))
rnaIds = sim_data.process.transcription.rnaData["id"][
sim_data.relation.rnaIndexToMonomerMapping]
proteinIds = sim_data.process.translation.monomerData["id"]
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
bulkMoleculeCounts = bulkMolecules.readColumn("counts")
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnaIndexes = np.array(
[moleculeIds.index(moleculeId) for moleculeId in rnaIds], np.int)
rnaCountsBulk = bulkMoleculeCounts[:, rnaIndexes]
proteinIndexes = np.array(
[moleculeIds.index(moleculeId) for moleculeId in proteinIds],
np.int)
proteinCountsBulk = bulkMoleculeCounts[:, proteinIndexes]
bulkMolecules.close()
relativeMRnaCounts = rnaCountsBulk[
-1, :] #/ rnaCountsBulk[-1, :].sum()
relativeProteinCounts = proteinCountsBulk[
-1, :] #/ proteinCountsBulk[-1, :].sum()
plt.figure(figsize=(8.5, 11))
plt.plot(relativeMRnaCounts,
relativeProteinCounts,
'o',
markeredgecolor='k',
markerfacecolor='none')
plt.xlabel("RNA count (at final time step)")
plt.ylabel("Protein count (at final time step)")
# plt.show()
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
sim_data = cPickle.load(open(simDataFile, "r"))
trpIdx = sim_data.moleculeGroups.aaIDs.index("TRP[c]")
growthLimits = TableReader(os.path.join(simOutDir, "GrowthLimits"))
trpRequests = growthLimits.readColumn("aaRequestSize")[BURN_IN:, trpIdx]
growthLimits.close()
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
trpSynIdx = moleculeIds.index("TRYPSYN[c]")
trpSynCounts = bulkMolecules.readColumn("counts")[BURN_IN:, trpSynIdx]
bulkMolecules.close()
trpSynKcat = 2**( (37. - 25.) / 10.) * 4.1 # From PMID 6402362 (kcat of 4.1/s measured at 25 C)
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time")[BURN_IN:] - initialTime
timeStep = TableReader(os.path.join(simOutDir, "Main")).readColumn("timeStepSec")[BURN_IN:]
trpSynMaxCapacity = trpSynKcat * trpSynCounts * timeStep
plt.figure(figsize = (8.5, 11))
plt.subplot(3, 1, 1)
plt.plot(time / 60., trpSynMaxCapacity, linewidth = 2)
plt.ylabel("Tryptophan Synthase Max Capacity")
plt.subplot(3, 1, 2)
plt.plot(time / 60., trpRequests, linewidth = 2)
plt.ylabel("TRP requested by translation")
plt.subplot(3, 1, 3)
plt.plot(time / 60., trpSynMaxCapacity / trpRequests, linewidth = 2)
plt.xlabel("Time (min)")
plt.ylabel("(Max capacity) / (Request)")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, "seedOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
ap = AnalysisPaths(seedOutDir, multi_gen_plot = True)
# Get all cells
allDir = ap.get_cells()
massNames = [
"dryMass",
"proteinMass",
#"tRnaMass",
"rRnaMass",
'mRnaMass',
"dnaMass"
]
cleanNames = [
"Dry\nmass",
"Protein\nmass",
#"tRNA\nmass",
"rRNA\nmass",
"mRNA\nmass",
"DNA\nmass"
]
fig, axesList = plt.subplots(len(massNames), sharex = True)
for simDir in allDir:
simOutDir = os.path.join(simDir, "simOut")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time")
mass = TableReader(os.path.join(simOutDir, "Mass"))
for idx, massType in enumerate(massNames):
massToPlot = mass.readColumn(massNames[idx])
axesList[idx].plot(time / 60. / 60., massToPlot, linewidth = 2)
axesList[idx].set_ylabel(cleanNames[idx] + " (fg)")
for axes in axesList:
axes.get_ylim()
axes.set_yticks(list(axes.get_ylim()))
axesList[0].set_title("Cell mass fractions")
axesList[len(massNames) - 1].set_xlabel("Time (hr)")
plt.subplots_adjust(hspace = 0.2, wspace = 0.5)
exportFigure(plt, plotOutDir, plotOutFileName,metadata)
plt.close("all")
def do_plot(self, variantDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(variantDir):
raise Exception, "variantDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
# Get all cells in each seed
ap = AnalysisPaths(variantDir, cohort_plot = True)
max_cells_in_gen = 0
for genIdx in range(ap.n_generation):
n_cells = len(ap.get_cells(generation = [genIdx]))
if n_cells > max_cells_in_gen:
max_cells_in_gen = n_cells
fig, axesList = plt.subplots(ap.n_generation, sharey = True, sharex = True,
subplot_kw={'aspect': 0.4, 'adjustable': 'box'})
initial_masses = np.zeros((max_cells_in_gen, ap.n_generation))
final_masses = np.zeros((max_cells_in_gen, ap.n_generation))
for genIdx in range(ap.n_generation):
gen_cells = ap.get_cells(generation = [genIdx])
for simDir in gen_cells:
simOutDir = os.path.join(simDir, "simOut")
mass = TableReader(os.path.join(simOutDir, "Mass"))
cellMass = mass.readColumn("cellMass")
initial_masses[np.where(simDir == gen_cells)[0], genIdx] = cellMass[0] / 1000.
final_masses[np.where(simDir == gen_cells)[0], genIdx] = cellMass[-1] / 1000.
# Plot initial vs final masses
if ap.n_generation == 1:
axesList = [axesList]
for idx, axes in enumerate(axesList):
axes.plot(initial_masses[:, idx], final_masses[:, idx], 'o')
z = np.polyfit(initial_masses[:, idx], final_masses[:, idx], 1)
p = np.poly1d(z)
axes.plot(initial_masses[:, idx], p(initial_masses[:, idx]), '--')
text_x = np.mean(axes.get_xlim())
text_y = np.mean(axes.get_ylim()) + np.mean(axes.get_ylim())*0.1
axes.text(text_x, text_y, r"$m_f$=%.3f$\times$$m_i$ + %.3f" % (z[0], z[1]))
axesList[-1].set_xlabel("Initial mass (pg)")
axesList[ap.n_generation / 2].set_ylabel("Final mass (pg)")
plt.subplots_adjust(hspace = 0.2, wspace = 0.5)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
bulkMoleculeCounts = bulkMolecules.readColumn("counts")
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnapId = "APORNAP-CPLX[c]"
rnapIndex = moleculeIds.index(rnapId)
rnapCountsBulk = bulkMoleculeCounts[:, rnapIndex]
RNAP_RNA_IDS = ["EG10893_RNA[c]", "EG10894_RNA[c]", "EG10895_RNA[c]", "EG10896_RNA[c]"]
rnapRnaIndexes = np.array([moleculeIds.index(rnapRnaId) for rnapRnaId in RNAP_RNA_IDS], np.int)
rnapRnaCounts = bulkMoleculeCounts[:, rnapRnaIndexes]
bulkMolecules.close()
uniqueMoleculeCounts = TableReader(os.path.join(simOutDir, "UniqueMoleculeCounts"))
rnapIndex = uniqueMoleculeCounts.readAttribute("uniqueMoleculeIds").index("activeRnaPoly")
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
nActive = uniqueMoleculeCounts.readColumn("uniqueMoleculeCounts")[:, rnapIndex]
uniqueMoleculeCounts.close()
plt.figure(figsize = (8.5, 11))
plt.subplot(5, 1, 1)
plt.plot(time / 60., nActive + rnapCountsBulk)
plt.xlabel("Time (min)")
plt.ylabel("Protein Counts")
plt.title("RNA Polymerase")
for subplotIdx in xrange(2, 6):
rnapRnaCountsIdx = subplotIdx - 2
plt.subplot(5, 1, subplotIdx)
plt.plot(time / 60., rnapRnaCounts[:, rnapRnaCountsIdx])
plt.xlabel("Time (min)")
plt.ylabel("mRNA counts")
plt.title(RNAP_RNA_IDS[rnapRnaCountsIdx])
plt.subplots_adjust(hspace = 0.5, top = 0.95, bottom = 0.05)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
# Exchange flux
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
fba_results = TableReader(os.path.join(simOutDir, "FBAResults"))
exFlux = fba_results.readColumn("externalExchangeFluxes")
exMolec = fba_results.readAttribute("externalMoleculeIDs")
moleculeIDs = ["GLC[p]", "OXYGEN-MOLECULE[p]"]
# Plot
fig = plt.figure(figsize = (8, 11.5))
rows = len(moleculeIDs)
cols = 1
for index, molecule in enumerate(["GLC[p]", "OXYGEN-MOLECULE[p]"]):
if molecule not in exMolec:
continue
moleculeFlux = -1. * exFlux[:, exMolec.index(molecule)]
ax = plt.subplot(rows, cols, index + 1)
ax.plot(time / 60. / 60., moleculeFlux)
averageFlux = np.average(moleculeFlux)
yRange = np.min([np.abs(np.max(moleculeFlux) - averageFlux), np.abs(np.min(moleculeFlux) - averageFlux)])
ymin = np.round(averageFlux - yRange)
ymax = np.round(averageFlux + yRange)
ax.set_ylim([ymin, ymax])
abs_max = np.max(moleculeFlux)
abs_min = np.min(moleculeFlux)
plt.figtext(0.7, 1. / float(rows) * 0.7 + (rows - 1 - index) / float(rows),
"Max: %s\nMin: %s" % (abs_max, abs_min), fontsize = 8)
ax.set_ylabel("External %s\n(mmol/gDCW/hr)" % molecule, fontsize = 8)
ax.set_xlabel("Time (hr)", fontsize = 8)
ax.set_title("%s" % molecule, fontsize = 10, y = 1.1)
ax.tick_params(labelsize = 8, which = "both", direction = "out")
plt.subplots_adjust(hspace = 0.5, wspace = 1)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
# Get the names of rnas from the KB
sim_data = cPickle.load(open(simDataFile, "rb"))
isTRna = sim_data.process.transcription.rnaData["isTRna"]
rnaIds = sim_data.process.transcription.rnaData["id"][isTRna]
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnaIndexes = np.array([moleculeIds.index(moleculeId) for moleculeId in rnaIds], np.int)
rnaCountsBulk = bulkMolecules.readColumn("counts")[:, rnaIndexes]
bulkMolecules.close()
# avgCounts = rnaCountsBulk.mean(0)
# relativeCounts = avgCounts / avgCounts.sum()
# relativeCounts = rnaCountsBulk[-1, :] / rnaCountsBulk[-1, :].sum()
plt.figure(figsize = (8.5, 11))
counts = rnaCountsBulk[-1, :]
expectedCountsArbitrary = sim_data.process.transcription.rnaExpression[sim_data.condition][isTRna]
expectedCounts = expectedCountsArbitrary/expectedCountsArbitrary.sum() * counts.sum()
maxLine = 1.1 * max(expectedCounts.max(), counts.max())
plt.plot([0, maxLine], [0, maxLine], '--r')
plt.plot(expectedCounts, counts, 'o', markeredgecolor = 'k', markerfacecolor = 'none')
plt.xlabel("Expected tRNA count (scaled to total)")
plt.ylabel("Actual tRNA count (at final time step)")
# plt.show()
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, "seedOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
if DISABLED:
print "Currently disabled because it requires too much memory."
return
ap = AnalysisPaths(seedOutDir, multi_gen_plot=True)
# Get all cells
allDir = ap.get_cells()
for simDir in allDir:
simOutDir = os.path.join(simDir, "simOut")
time = TableReader(os.path.join(simOutDir,
"Main")).readColumn("time")
counts = TableReader(os.path.join(
simOutDir, "BulkMolecules")).readColumn("counts")
countsToMolar = TableReader(
os.path.join(simOutDir,
"EnzymeKinetics")).readColumn("countsToMolar")
allNames = TableReader(os.path.join(
simOutDir, "BulkMolecules")).readAttribute('objectNames')
compoundNames = []
nonZeroCounts = counts.T[np.any(counts.T, axis=1)]
for idx, counts in enumerate(nonZeroCounts):
if (counts[BURN_IN_SECONDS:] > 0).sum() > 100:
compartment = allNames[idx][-3:]
compoundNames.append(allNames[idx][:20])
concentrations = (counts * countsToMolar)
if time[0] < 1:
concentrations[:BURN_IN_SECONDS] = np.mean(
concentrations[BURN_IN_SECONDS:])
plt.plot(time / 60.,
concentrations / np.mean(concentrations))
# plt.legend(compoundNames, fontsize=5)
plt.title("Protein Concentrations")
plt.xlabel("Time (min)")
plt.ylabel("Mean-normalized concentration")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, seedOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(seedOutDir):
raise Exception, "seedOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
ap = AnalysisPaths(seedOutDir, multi_gen_plot=True)
# TODO: Declutter Y-axis
# Get all cells
allDir = ap.get_cells().tolist()
massNames = [
"dryMass",
]
cleanNames = [
"Dry\nmass",
]
for simDir in allDir:
simOutDir = os.path.join(simDir, "simOut")
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
mass = TableReader(os.path.join(simOutDir, "Mass"))
for idx, massType in enumerate(massNames):
massToPlot = mass.readColumn(massNames[idx])
f = plt.figure(figsize=(1.25, 0.8), frameon=False)
ax = f.add_axes([0, 0, 1, 1])
ax.axis("off")
ax.plot(time, massToPlot, linewidth=2)
ax.set_ylim([massToPlot.min(), massToPlot.max()])
ax.set_xlim([time.min(), time.max()])
exportFigure(
plt, plotOutDir,
"r01_{}_gen{}".format(massType, allDir.index(simDir)))
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
processNames = bulkMolecules.readAttribute("processNames")
atpAllocatedInitial = bulkMolecules.readColumn("atpAllocatedInitial")
atpRequested = bulkMolecules.readColumn("atpRequested")
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
bulkMolecules.close()
# Plot
plt.figure(figsize = (8.5, 11))
rows = 7
cols = 2
for processIndex in np.arange(len(processNames)):
ax = plt.subplot(rows, cols, processIndex + 1)
ax.plot(time / 60., atpAllocatedInitial[:, processIndex])
ax.plot(time / 60., atpRequested[:, processIndex])
ax.set_title(str(processNames[processIndex]), fontsize = 8, y = 0.85)
ymin = np.amin([atpAllocatedInitial[:, processIndex], atpRequested[:, processIndex]])
ymax = np.amax([atpAllocatedInitial[:, processIndex], atpRequested[:, processIndex]])
ax.set_ylim([ymin, ymax])
ax.set_yticks([ymin, ymax])
ax.set_yticklabels(["%0.2e" % ymin, "%0.2e" % ymax])
ax.spines['top'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.xaxis.set_ticks_position('bottom')
ax.tick_params(which = 'both', direction = 'out', labelsize = 6)
# ax.set_xticks([])
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
plt.subplots_adjust(hspace = 2.0, wspace = 2.0)
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
timeStepSec = TableReader(os.path.join(simOutDir, "Main")).readColumn("timeStepSec")
fba_results = TableReader(os.path.join(simOutDir, "FBAResults"))
exFlux = fba_results.readColumn("externalExchangeFluxes")
exMolec = fba_results.readAttribute("externalMoleculeIDs")
fba_results.close()
mass = TableReader(os.path.join(simOutDir, "Mass"))
processMassDifferences = mass.readColumn("processMassDifferences")
cellMass = mass.readColumn("dryMass")
mass.close()
exchangeMasses = {} # some duplicates in exMolec like CO2 and water so create dict to avoid double counting
raw_data = KnowledgeBaseEcoli()
for metabolite in raw_data.metabolites:
for molecID in exMolec:
if molecID.split("[")[0] == "WATER":
exchangeMasses[molecID] = 18.015 * exFlux[:,exMolec.index(molecID)] * 10**-3 * cellMass * timeStepSec / 60 / 60
if molecID.split("[")[0] == metabolite["id"]:
exchangeMasses[molecID] = metabolite["mw7.2"] * exFlux[:,exMolec.index(molecID)] * 10**-3 * cellMass * timeStepSec / 60 / 60
massInflux = 0
for molecID in exchangeMasses.keys():
massInflux += exchangeMasses[molecID]
massProduced = processMassDifferences[:,0] # in metabolism
massDiff = massInflux + massProduced
plt.plot(time / 60. / 60., -massDiff)
plt.tick_params(axis='both', which='major', labelsize=10)
plt.ylabel("Mass Accumulation per time step (fg)")
plt.title("Mass imported - mass created in metabolism process")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
sim_data = cPickle.load(open(simDataFile, "rb"))
fbaResults = TableReader(os.path.join(simOutDir, "FBAResults"))
externalExchangeFluxes = fbaResults.readColumn("externalExchangeFluxes")
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
timeStepSec = TableReader(os.path.join(simOutDir, "Main")).readColumn("timeStepSec")
externalMoleculeIDs = np.array(fbaResults.readAttribute("externalMoleculeIDs"))
fbaResults.close()
if GLUCOSE_ID not in externalMoleculeIDs:
print "This plot only runs when glucose is the carbon source."
return
glucoseIdx = np.where(externalMoleculeIDs == GLUCOSE_ID)[0][0]
glucoseFlux = FLUX_UNITS * externalExchangeFluxes[:, glucoseIdx]
mass = TableReader(os.path.join(simOutDir, "Mass"))
cellMass = MASS_UNITS * mass.readColumn("cellMass")
cellDryMass = MASS_UNITS * mass.readColumn("dryMass")
growth = GROWTH_UNITS * mass.readColumn("growth") / timeStepSec
mass.close()
glucoseMW = sim_data.getter.getMass([GLUCOSE_ID])[0]
glucoseMassFlux = glucoseFlux * glucoseMW * cellDryMass
glucoseMassYield = growth / -glucoseMassFlux
fig = plt.figure(figsize = (8.5, 11))
plt.plot(time, glucoseMassYield)
plt.xlabel("Time (s)")
plt.ylabel("g cell / g glucose")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
rnapId = "APORNAP-CPLX[c]"
rnapIndex = moleculeIds.index(rnapId)
rnapCountsBulk = bulkMolecules.readColumn("counts")[:, rnapIndex]
bulkMolecules.close()
uniqueMoleculeCounts = TableReader(
os.path.join(simOutDir, "UniqueMoleculeCounts"))
rnapIndex = uniqueMoleculeCounts.readAttribute(
"uniqueMoleculeIds").index("activeRnaPoly")
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
nActive = uniqueMoleculeCounts.readColumn(
"uniqueMoleculeCounts")[:, rnapIndex]
uniqueMoleculeCounts.close()
plt.figure(figsize=(8.5, 11))
plt.plot(time / 60., nActive * 100. / (nActive + rnapCountsBulk))
#plt.axis([0,60,0,25])
plt.xlabel("Time (min)")
plt.ylabel("Percent of RNA Polymerase Molecules that are Active")
plt.title("Active RNA Polymerase Percentage")
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
sim_data = cPickle.load(open(simDataFile))
aaIDs = sim_data.moleculeGroups.aaIDs
aaIndexes = np.array([moleculeIds.index(aaId) for aaId in aaIDs],
np.int)
aaCounts = bulkMolecules.readColumn("counts")[:, aaIndexes]
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
bulkMolecules.close()
plt.figure(figsize=(8.5, 11))
for idx in xrange(21):
plt.subplot(6, 4, idx + 1)
plt.plot(time / 60., aaCounts[:, idx], linewidth=2)
plt.xlabel("Time (min)")
plt.ylabel("Counts")
plt.title(aaIDs[idx])
plt.subplots_adjust(hspace=0.5, wspace=0.5)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile,
validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
NTP_IDS = ['ATP[c]', 'CTP[c]', 'GTP[c]', 'UTP[c]']
ntpIndexes = np.array([moleculeIds.index(ntpId) for ntpId in NTP_IDS],
np.int)
ntpCounts = bulkMolecules.readColumn("counts")[:, ntpIndexes]
initialTime = TableReader(os.path.join(
simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(
simOutDir, "Main")).readColumn("time") - initialTime
bulkMolecules.close()
plt.figure(figsize=(8.5, 11))
for idx in xrange(4):
plt.subplot(2, 2, idx + 1)
plt.plot(time / 60., ntpCounts[:, idx], linewidth=2)
plt.xlabel("Time (min)")
plt.ylabel("Counts")
plt.title(NTP_IDS[idx])
print "NTPs required for cell division (nt/cell-cycle) = %d" % sum(
ntpCounts[0, :])
plt.subplots_adjust(hspace=0.5)
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")
def do_plot(self, simOutDir, plotOutDir, plotOutFileName, simDataFile, validationDataFile, metadata):
if not os.path.isdir(simOutDir):
raise Exception, "simOutDir does not currently exist as a directory"
if not os.path.exists(plotOutDir):
os.mkdir(plotOutDir)
bulkMolecules = TableReader(os.path.join(simOutDir, "BulkMolecules"))
moleculeIds = bulkMolecules.readAttribute("objectNames")
RIBOSOME_RNA_IDS = ["RRLA-RRNA[c]", "RRSA-RRNA[c]", "RRFA-RRNA[c]"]
ribosomeRnaIndexes = np.array([moleculeIds.index(rRnaId) for rRnaId in RIBOSOME_RNA_IDS], np.int)
ribosomeRnaCountsBulk = bulkMolecules.readColumn("counts")[:, ribosomeRnaIndexes]
bulkMolecules.close()
uniqueMoleculeCounts = TableReader(os.path.join(simOutDir, "UniqueMoleculeCounts"))
ribosomeIndex = uniqueMoleculeCounts.readAttribute("uniqueMoleculeIds").index("activeRibosome")
initialTime = TableReader(os.path.join(simOutDir, "Main")).readAttribute("initialTime")
time = TableReader(os.path.join(simOutDir, "Main")).readColumn("time") - initialTime
nActive = uniqueMoleculeCounts.readColumn("uniqueMoleculeCounts")[:, ribosomeIndex]
uniqueMoleculeCounts.close()
plt.figure(figsize = (8.5, 11))
plt.plot(time / 60, nActive)
plt.plot([time[0] / 60., time[-1] / 60.], [2 * nActive[0], 2 * nActive[0]], "r--")
plt.xlabel("Time (min)")
plt.ylabel("Counts")
plt.title("Active Ribosomes Final:Initial = %0.2f" % (nActive[-1] / float(nActive[0])))
exportFigure(plt, plotOutDir, plotOutFileName, metadata)
plt.close("all")