Now jupyter installed on the server and I am using below code to plot the rarefaction plot but I am still getting some error. could you please suggest how I can get rid of it?
#Run it in jupyter lab or notebook
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
import numpy as np
import os
#%matplotlib inline
qza = 'alpha-rarefaction-20000.qzv' # path to rarefaction file from qiime2
os.system("unzip qza")
digest = a[1].split('/')[0].replace(' inflating: ','')
inf = digest + '/data/observed_otus.csv'
otus = pd.read_csv(inf,index_col=0, sep=',')
os.system('rm -r $digest')
cols = [col for col in otus.columns if 'iter' not in col]
mean,data = otus[cols],pd.DataFrame(columns=cols)
depths = [col.split('_')[0] for col in otus.columns if 'depth' in col]
otus = otus.drop(cols,axis=1)
otus.columns = depths
for depth in depths:
mean['ASV'] = otus[depth].mean(axis=1)
mean['depth']= depth.split('-')[-1]
data = pd.concat([data,mean])
# here provide colors for each item that will be plotted
pal={'Irrigated':'brown','Rainfed':'red'}
fig,ax = plt.subplots(figsize=(2.5,2),dpi=600,tight_layout=True)
sns.set(style='ticks',rc={"lines.linewidth":0.7,"axes.linewidth":0.5})
# use your column name to plot here
sns.lineplot(x='depth',y='ASV',data=data,palette=pal,hue='Season',sort=False,err_style='bars',\
dashes=True,style='Season',ci=67)
ax.set_xlabel('Sequencing depth',fontsize=8)
ax.set_ylabel('Observed ASVs',fontsize=8)
ax.tick_params(axis='x', labelrotation=90)
ax.tick_params(axis='both',which='major',length=2,pad=0.5,labelsize=6)
handles, labels = ax.get_legend_handles_labels()
ax.legend(handles=handles[1:],labels=labels[1:],fontsize=5,frameon=False,numpoints=4,borderaxespad=0,handletextpad=0.2,loc=2,)
plt.savefig('Infected_observed_ASVs.png', bbox_inches='tight')
Error;
$ python3 myscript.rarefaction.py
Traceback (most recent call last):
File "myscript.rarefaction.py", line 4, in <module>
import seaborn as sns
File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/__init__.py", line 2, in <module>
from .rcmod import * # noqa: F401,F403
File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/rcmod.py", line 7, in <module>
from . import palettes
File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/palettes.py", line 9, in <module>
from .utils import desaturate, get_color_cycle
File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/seaborn/utils.py", line 11, in <module>
import pandas as pd
File "/opt/apps/seaborn/0.11.0/python3-3.7.4/lib/python3.7/site-packages/pandas/__init__.py", line 11, in <module>
__import__(dependency)
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 1101, in <module>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/lazy.py", line 101, in _lazy
File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 1098, in <genexpr>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 114, in resource_exists
File "/opt/gridware/depots/54e7fb3c/el7/pkg/libs/matplotlib_python34/1.5.1/gcc-4.8.5+python3-3.4.3+numpy_python34-1.11.3/python/lib/python3.4/site-packages/pytz-2019.1-py3.4.egg/pytz/__init__.py", line 102, in open_resource
File "<frozen importlib._bootstrap>", line 983, in _find_and_load
File "<frozen importlib._bootstrap>", line 967, in _find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 668, in _load_unlocked
File "<frozen importlib._bootstrap>", line 638, in _load_backward_compatible
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2927, in <module>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2913, in _call_aside
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2952, in _initialize_master_working_set
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 956, in subscribe
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2952, in <lambda>
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2515, in activate
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2097, in declare_namespace
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2047, in _handle_ns
File "/opt/gridware/depots/54e7fb3c/el7/pkg/apps/setuptools/24.0.1/python-2.7.8/python/lib/python2.7/site-packages/setuptools-24.0.1-py2.7.egg/pkg_resources/__init__.py", line 2066, in _rebuild_mod_path
AttributeError: '_NamespacePath' object has no attribute 'sort'
metadata file ;
#SampleID Villages Region Treatment Batch Season
PN0086D.1.S1 Kholabari Mymensingh T1 batch1 Irrigated
PN0086D.2.S2 Bogajan Mymensingh T1 batch1 Irrigated
PN0086D.3.S3 Bonkua Mymensingh T1 batch1 Irrigated