def rconnect( self, creator = None ):
'''open connection within R to database.'''
if not self.rdb:
R.library( 'RSQLite' )
if creator:
self.rdb = creator()
else:
if self.backend.startswith( 'sqlite' ):
self.rdb = R.dbConnect(R.SQLite(), dbname=re.sub( "sqlite:///./", "", self.backend ) )
else:
raise NotImplementedError("can not connect to %s in R" % self.backend )
#This bit connects to R and gets the information itself.
from rpy2 import *
from rpy2.robjects import r
f = open('rdata.dat', 'r')
r.library("RMySQL")
#This is how you shouldn't ever code.
database = "select "
database += sys.argv[4]
database += " from "
database += sys.argv[2]
print database
#Connect to the database. Note, this requires Sequel Pro, probably.
con=r.dbConnect(r.MySQL(),user="******",password="******",dbname="myExperiment",host="127.0.0.1",port=8889)
data=r.dbGetQuery(con, database)
#All it is used for is to get the length, because that's a common problem.
row = r.length(data[0])
#This is the first hardcoded graph, with all of the tags combined. It needs some work, I think.
def printfirst():
print("#"+sys.argv[2] + " " + sys.argv[3] + " (All) by "+sys.argv[4]+"\n data=dbGetQuery(con,\"select "+sys.argv[3]+", "+sys.argv[4]+" from " + sys.argv[2] + "\")\n ggplot(data,aes("+sys.argv[3]+", "+sys.argv[4]+")) + geom_boxplot() +xlab(\"All "+sys.argv[3]+"\") +ylab(\""+sys.argv[4]+"\")\n file = ggplot(data,aes("+sys.argv[3]+", "+sys.argv[4]+")) + geom_boxplot() +xlab(\"All "+sys.argv[3]+"\") +ylab(\""+sys.argv[4]+"\")\n ggsave(file, file=\""+sys.argv[2]+"_"+sys.argv[3]+"_all_"+sys.argv[4]+".png\")\n \n")
output.write("#"+sys.argv[2] + " " + sys.argv[3] + " (All) by "+sys.argv[4]+"\n data=dbGetQuery(con,\"select "+sys.argv[3]+", "+sys.argv[4]+" from " + sys.argv[2] + "\")\n ggplot(data,aes("+sys.argv[3]+", "+sys.argv[4]+")) + geom_boxplot() +xlab(\"All "+sys.argv[3]+"\") +ylab(\""+sys.argv[4]+"\")\n file = ggplot(data,aes("+sys.argv[3]+", "+sys.argv[4]+")) + geom_boxplot() +xlab(\"All "+sys.argv[3]+"\") +ylab(\""+sys.argv[4]+"\")\n ggsave(file, file=\""+sys.argv[2]+"_"+sys.argv[3]+"_all_"+sys.argv[4]+".png\")\n \n")
#Print it.
printfirst()
#This is the hardcode that actually results in the R code.
#I wouldn't suggest looking too hard at it, argv isn't pretty.
for x in range(len(graph)):