In [1]:

    

# paths
import os

workDir = '/home/nick/notebook/SIPSim/dev/bac_genome1147/'
buildDir = os.path.join(workDir, 'atomIncorp_taxaIncorp')
R_dir = '/home/nick/notebook/SIPSim/lib/R/'

fragFile = '/home/nick/notebook/SIPSim/dev/bac_genome1147/validation/ampFrags_kde.pkl'
genome_index = '/var/seq_data/ncbi_db/genome/Jan2016/bac_complete_spec-rep1_rn/genome_index.txt'


    

In [2]:

    

import glob
import itertools
import nestly


    

In [3]:

    

%load_ext rpy2.ipython
%load_ext pushnote


    

In [4]:

    

%%R
library(ggplot2)
library(dplyr)
library(tidyr)
library(gridExtra)


    

    




/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: Stackoverflow is a great place to get help:
http://stackoverflow.com/tags/ggplot2.

  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: 
Attaching package: ‘dplyr’


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:stats’:

    filter, lag


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: 
Attaching package: ‘gridExtra’


  res = super(Function, self).__call__(*new_args, **new_kwargs)
/opt/anaconda/lib/python2.7/site-packages/rpy2/robjects/functions.py:106: UserWarning: The following object is masked from ‘package:dplyr’:

    combine


  res = super(Function, self).__call__(*new_args, **new_kwargs)