comparison hetbox.py @ 2:57c5ea9c3c5c draft

Uploaded

1:b4f9a4f2f65d

# New in this version:
# - Add in proper header line if not present

import os
import sys
import numpy
from rpy2.robjects import Formula
from rpy2.robjects.packages import importr
from rpy2 import robjects

  if 'SAMPLE' not in labels or labels[11] != 'MINOR.FREQ.PERC.':
    sys.stderr.write("Error: Input file does not seem to have a proper header "
      +"line.\nAdding an artificial header..")
    add_header = True

base = importr('base')
utils = importr('utils')
stats = importr('stats')
rprint = robjects.globalenv.get("print")
graphics = importr('graphics')

# Formula() creates a Python object representing the R object returned by x ~ y
formula = Formula('minor_freq ~ samples')
# The "environment" in .getenvironment() is the entire R workspace in which the
# Formula object exists. The R workspace meaning all the defined variables.
# Here, the .getenvironment() method is being used to set some variables in the

# R workspace
formula.getenvironment()['minor_freq'] = minor_freq
formula.getenvironment()['samples']    = samples

# create boxplot - fill kwargs1 with the options for the boxplot function
kwargs1 = {'ylab':"Minor allele frequency (%)", 'col':"gray", 'xaxt':"n",
           'outpch':"*",'main':"Distribution of minor allele frequencies",
           'cex.lab':"1.5"}
p = graphics.boxplot(formula, **kwargs1)
table  = base.table(DATA.rx2('SAMPLE'))
graphics.text(0.5, 1, 'N:', font=2)
for i in range(1, base.length(table)[0]+1, 1):
    graphics.text(i, 1, table[i-1], font=2)

graphlabels = base.names(table)
kwargs3 = {'pos':"0", 'las':"2", 'cex.axis':"1"}
graphics.axis(1, at=range(1, len(graphlabels)+1, 1), labels=graphlabels, **kwargs3)
grdevices.dev_off()

if not report:
  sys.exit(0)

2:57c5ea9c3c5c

# New in this version:
# - Add in proper header line if not present

import os
import sys
import array
import numpy
from rpy2.robjects import Formula
from rpy2.robjects.packages import importr
from rpy2 import robjects

  if 'SAMPLE' not in labels or labels[11] != 'MINOR.FREQ.PERC.':
    sys.stderr.write("Error: Input file does not seem to have a proper header "
      +"line.\nAdding an artificial header..")
    add_header = True

r = robjects.r
base = importr('base')
utils = importr('utils')
stats = importr('stats')
rprint = robjects.globalenv.get("print")
graphics = importr('graphics')

# Formula() creates a Python object representing the R object returned by x ~ y
formula = Formula('minor_freq ~ samples')
# The "environment" in .getenvironment() is the entire R workspace in which the
# Formula object exists. The R workspace meaning all the defined variables.
# Here, the .getenvironment() method is being used to set some variables in the
# R workspace

formula.getenvironment()['minor_freq'] = minor_freq
formula.getenvironment()['samples']    = samples


r.par(oma=array.array('i', [0,0,0,0]))
r.par(mar=array.array('i', [10,4,4,2]))
ylimit = array.array('i',[-5,50])

# create boxplot - fill kwargs1 with the options for the boxplot function
kwargs1 = {'ylab':"Minor allele frequency (%)", 'col':"gray", 'xaxt':"n",
           'outpch':"*",'main':"Distribution of minor allele frequencies",
           'cex.lab':"1.5"}
p = graphics.boxplot(formula, axes=0,ylim=ylimit, lty=1,**kwargs1)

table = base.table(DATA.rx2('SAMPLE'))
#graphics.text(-1, 1, 'N:', font=2)
for i in range(1, base.length(table)[0]+1, 1):
    graphics.text(i, -1, table[i-1], font=2)

graphlabels = base.names(table)
kwargs3 = {'pos':"-2", 'las':"2", 'cex.axis':"1"}
graphics.axis(1, at=range(1, len(graphlabels)+1, 1),labels=graphlabels, **kwargs3)
graphics.axis(2,at=(range(0,60,10)),pos=0,font=2)
grdevices.dev_off()

if not report:
  sys.exit(0)