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require_relative '../../lazar/lib/lazar'
include OpenTox
#$mongo.database.drop
#$gridfs = $mongo.database.fs # recreate GridFS indexes
# compare duplicates within datasets
#old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mmol_corrected_smiles.csv")
old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mg_corrected_smiles_mmol.csv")
#new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL.csv")
new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL_mmol.csv")
#combined = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL-rat-combined.csv")
compound_vector = []
value_vector = []
dataset_vector = []
vars = []
[old, new].each do |dataset|
vars << []
#vars[dataset.name] = []
p dataset.name
p dataset.compounds.size
p dataset.duplicates(dataset.features.first).size
dataset.duplicates.each do |cid,values|
R.assign "values", values
var = R.eval("var(-log(values))").to_f
vars.last << var
#smi = Compound.find(cid).smiles
smi = cid.to_s
values.each do |val|
compound_vector << smi
value_vector << - Math.log(val)
dataset_vector << dataset.name
end
#vars << { :var => var, :values => values, :smiles => smi }
end
#vars.sort!{|a,b| a[:var] <=> b[:var]}
#vars.each do |dup|
#dup[:values].each do |v|
#compound_vector << dup[:smiles]
#value_vector << v
#end
#end
end
p vars
# TODO statistical test for variances
R.assign "vars1", vars[0]
R.assign "vars2", vars[1]
print "p-value: #{R.eval("t.test(vars1,vars2)$p.value").to_f}"
R.assign "smi", compound_vector
R.assign "values", value_vector
R.assign "dataset", dataset_vector
R.eval "df <- data.frame(factor(smi),values,factor(dataset))"
R.eval "df$smi <- reorder(df$factor.smi,df$values)"
R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))"
R.eval "img <- img + ylab('-log(LOAEL mg/kg_bw/day)') + xlab('Compound') + theme(axis.text.x = element_blank())"
R.eval "img <- img + geom_point()"
#R.eval "img <- img + scale_x_discrete(breaks=NULL) + geom_point() + coord_flip()"# + xlab('-log(LOAEL)'), ylab('Compound')"
#R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael_variance.svg', plot=img)"
R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-variance.svg', plot=img,width=12, height=8)"
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