def barplot(fn, tax, lim, ax, alpha):
new_rows, old_otus = gf.gf(fn, lim, tax, return_old_otus=True)
taxa = []
for a in range(len(old_otus)):
if a > 0:
if new_rows[a][0] == 'Clostridiales_vadinBB60_group':
new_rows[a][0] = 'Clostridiales'
if new_rows[a][0] == 'Incertae_Sedis':
new_rows[a][0] = 'Incertae Sedis'
if new_rows[a][0] == '$Kurtzmaniella-Candida_clade$':
new_rows[a][0] = '$Kurtzmaniella$'
if new_rows[a][0] == '$Thalassolituus$ $oleivorans$':
new_rows[a][0] = '$Thalassolituus$\n $oleivorans$'
name = old_otus[a] + ' ' + new_rows[a][0]
if name == 'ASV2 Bacteria':
name = 'ASV2 $(Spirochaeta)$'
if name == 'ASV125 Bacteria':
name = 'ASV125 $(Thermobrachium)$'
if name == 'ASV1 Eukaryota':
name = 'ASV1 $(Cafeteria)$'
if name == 'ASV2 Eukaryota':
name = 'ASV2 $(Cafeteria)$'
if name == 'ASV35 Eukaryota':
name = 'ASV35 $(Oxyrrhis$ $marina)$'
taxa.append(name)
taxa.append(new_rows[-1][0])
samples = []
for b in range(len(new_rows)):
if b > 0:
samples.append(new_rows[b][1:])
data = numpy.array(samples)
bottom = numpy.cumsum(data, axis=0)
x = [1, 2, 3, 4]
colors = get_distinct_colors(len(samples))
ax.bar(x, data[0], color=colors[0], label=taxa[0], alpha=alpha)
for j in range(1, data.shape[0]):
ax.bar(x,
data[j],
color=colors[j],
bottom=bottom[j - 1],
label=taxa[j],
alpha=alpha)
ax.set_ylim([0, 100])
if ax == l16S:
ax.legend(bbox_to_anchor=(2.2, 1.01), fontsize=7)
elif ax == l18S:
ax.legend(bbox_to_anchor=(2.09, 1.01), fontsize=7)
ax.set_xlim([0.8, 5])
plt.setp(ax, xticks=[1.4, 2.4, 3.4, 4.4], xticklabels=[1, 2, 3, 4])
return
def barplot(fn, tax, lim, ax, alpha):
new_rows, old_otus = gf.gf(fn, lim, tax, return_old_otus=True)
taxa = []
for a in range(len(old_otus)):
if a > 0:
if new_rows[a][0] == 'Clostridiales_vadinBB60_group':
new_rows[a][0] = 'Clostridiales'
if new_rows[a][0] == 'Incertae_Sedis':
new_rows[a][0] = 'Incertae Sedis'
if new_rows[a][0] == '$Kurtzmaniella-Candida_clade$':
new_rows[a][0] = '$Kurtzmaniella$'
if new_rows[a][0] == '$Thalassolituus$ $oleivorans$':
new_rows[a][0] = '$Thalassolituus$\n $oleivorans$'
name = old_otus[a] + ' ' + new_rows[a][0]
if name == 'ASV2 Bacteria':
name = 'ASV2 $(Spirochaeta)$'
if name == 'ASV125 Bacteria':
name = 'ASV125 $(Thermobrachium)$'
if name == 'ASV1 Eukaryota':
name = 'ASV1 $(Cafeteria)$'
if name == 'ASV2 Eukaryota':
name = 'ASV2 $(Cafeteria)$'
if name == 'ASV35 Eukaryota':
name = 'ASV35 $(Oxyrrhis$ $marina)$'
taxa.append(name)
taxa.append(new_rows[-1][0])
samples = []
for b in range(len(new_rows)):
if b > 0:
samples.append(new_rows[b][1:])
data = numpy.array(samples)
bottom = numpy.cumsum(data, axis=0)
x = [1, 2, 3, 4, 5]
if ax == l16S:
colors = [
(0.9784561615118298, 0.8544526316405848, 0.11043145241311547),
(0.20015147663099214, 0.9752845415843673, 0.1405258562499635),
(0.2355334788858654, 0.9602365332487572, 0.9602365332487575),
(0.5692453105690995, 0.9795050492777015, 0.1589855718604971),
(0.5824628057375845, 0.18474425574558218, 0.9801813557295874),
(0.1533182103913031, 0.6371021121284499, 0.99994003843131),
(0.1512473190618882, 0.08807742030502586, 0.9724560029011022),
(0.9669797640117426, 0.5223094007170633, 0.18880662824605388),
(0.1633168997160368, 0.820010933188215, 0.9991093059533547),
(0.14608558739885424, 0.4403676619617287, 0.9700753961749042),
(0.21710576449418473, 0.9626100823361772, 0.4833573065806109),
(0.11414594323754845, 0.9990088230852705, 0.8093953488321874),
(0.7489378889588101, 0.12358724124585263, 0.9990781480439929),
(0.9703040330592666, 0.17675506882904968, 0.8569398953120929),
(0.9209638926431851, 0.12839534652503937, 0.9819307038830429),
(0.9704780729631548, 0.6960071852119865, 0.2019595872598834),
(0.9968577762986314, 0.06298771658430391, 0.26310272938023116),
(0.2918368133300881, 0.9857160759840947, 0.014285108268485947),
(0.99807399645539, 0.02623618072940448, 0.02623618072940448),
(0.8978297835866152, 0.9620647138802005, 0.06277568977000492),
(0.9579720543054757, 0.3027723777165785, 0.12408155682869748),
(0.05840245005662492, 0.9786746791606609, 0.18986991135720163),
(0.40706716820400585, 0.1861479381611485, 0.9593652433111485),
(0.08413585895436615, 0.21115811584195723, 0.973291657167507),
(0.9941953083479688, 0.18928435172215308, 0.7067271095530344),
(0.9632776829039245, 0.05428066332342807, 0.4438508145722114),
(0.0644938369930973, 0.9829129205955643, 0.5893047419087928),
(0.7469534608075091, 0.9633040903295119, 0.20607688700250215)
]
alpha = 0.1
ax.bar(x,
data[0],
color=colors[0],
label=taxa[0],
alpha=alpha,
edgecolor='k')
for j in range(1, data.shape[0]):
ax.bar(x,
data[j],
color=colors[j],
bottom=bottom[j - 1],
label=taxa[j],
alpha=alpha,
edgecolor='k')
"""
if j == 2 or j == 3:
ax.bar(x, data[j], color=colors[j], bottom=bottom[j-1], label=taxa[j], alpha=1, edgecolor='k', linewidth=2)
#ax.bar(x[:3], data[j][:3], color=colors[j][:3], bottom=bottom[j-1][:3], label=taxa[j], alpha=1, edgecolor='k', linewidth=2)
#ax.bar(x[3:], data[j][3:], color=colors[j][3:], bottom=bottom[j-1][3:], alpha=alpha, edgecolor='k')
else:
ax.bar(x, data[j], color=colors[j], bottom=bottom[j-1], label=taxa[j], alpha=alpha, edgecolor='k')
"""
elif ax == l18S:
colors = [
(0.8046628587291401, 0.9847340964016936, 0.08437790803892675),
(0.16068100826509213, 0.812725598821964, 0.9757367464611822),
(0.6436875010120449, 0.14402242251126474, 0.9767975533458975),
(0.1711921518161551, 0.9803335451227438, 0.3330204304774728),
(0.15210023365541248, 0.9654221473432107, 0.6400933818680916),
(0.4831155384359089, 0.16674931260219694, 0.957664877186477),
(0.9807780937856913, 0.07931416136055469, 0.25960694784558197),
(0.9837397533803838, 0.09670477839123093, 0.45151876838689137),
(0.13182563895300092, 0.4646501037103113, 0.963886800846277),
(0.9890448336366396, 0.3479571614890893, 0.18768524345220172),
(0.9833610439316122, 0.8165161217478611, 0.14913643301285695),
(0.15788061367972028, 0.15788061367972028, 0.9684884132083601),
(0.22189305336408016, 0.9721974637542361, 0.5220148175201427),
(0.05962894416054154, 0.9749015092853106, 0.05962894416054154),
(0.9607155787073374, 0.9607155787073376, 0.17402712858047287),
(0.20871927804490387, 0.9655241879001555, 0.9655241879001557),
(0.9969160025600691, 0.16784646939971049, 0.996916002560069),
(0.9783492220943032, 0.6016522496924305, 0.03660679108962117),
(0.16896336774581666, 0.6425806369800509, 0.9583254831362071),
(0.983223988424602, 0.07534102345091298, 0.07534102345091298),
(0.634346909674582, 0.9700991345369391, 0.13071857238104656),
(0.0925429104376172, 0.2697573840925528, 0.9786152787122955),
(0.9750248939667724, 0.17051115981659548, 0.8141221471367364),
(0.9713266768301306, 0.520553637887629, 0.22003827859262792),
(0.07733748452818678, 0.9838852945756328, 0.8025757325661438),
(0.8034228927487032, 0.11352326761401266, 0.975897799032376),
(0.9880639417025762, 0.09028477322054818, 0.6289522743097649),
(0.23962110378416382, 0.9564484109039381, 0.06041427700422031),
(0.45009313460979883, 0.9676734612144107, 0.10503958354005771),
(0.3258338839894387, 0.16119823022031277, 0.9843764990659452)
]
alpha = 0.1
ax.bar(x,
data[0],
color=colors[0],
label=taxa[0],
alpha=0.5,
edgecolor='k',
linewidth=2)
for j in range(1, data.shape[0]):
if j == 0 or j == 1:
ax.bar(x,
data[j],
color=colors[j],
bottom=bottom[j - 1],
label=taxa[j],
alpha=0.5,
edgecolor='k',
linewidth=2)
else:
ax.bar(x,
data[j],
color=colors[j],
bottom=bottom[j - 1],
label=taxa[j],
alpha=alpha,
edgecolor='k')
#ax.bar(x, data[j], color=colors[j], bottom=bottom[j-1], label=taxa[j], alpha=alpha, edgecolor='k')
ax.set_ylim([0, 100])
if ax == l16S:
ax.legend(bbox_to_anchor=(2.13, 1.01), fontsize=7)
elif ax == l18S:
ax.legend(bbox_to_anchor=(1.1, 1.01), fontsize=7)
ax.set_xlim([0.5, 5.5])
plt.sca(ax)
#plt.xticks(x)
plt.setp(ax, xticks=[1, 2, 3, 4, 5], xticklabels=[0, 1, 2, 3, 4])
return