python/pymethylprocess/PreProcessDataTypes.py
def plot_qc_metrics(self, output_dir):
        """Plot QC results from ENmix pipeline and possible minfi. Still experimental.

        Parameters
        ----------
        output_dir
            Where to store plots."""
        self.enmix.plotCtrl(self.RGset)
        grdevice = importr("grDevices")
        geneplotter = importr("geneplotter")
        base = importr('base')
        anno=self.minfi.getAnnotation(self.RGset)
        anno_py = pandas2ri.ri2py(robjects.r['as'](anno,'data.frame'))
        beta_py = pandas2ri.ri2py(self.beta)
        beta1=numpy2ri.py2ri(beta_py[anno_py["Type"]=="I"])
        beta2=numpy2ri.py2ri(beta_py[anno_py["Type"]=="II"])
        grdevice.jpeg(output_dir+'/dist.jpg',height=900,width=600)
        base.par(mfrow=robjects.vectors.IntVector([3,2]))
        self.enmix.multidensity(self.beta, main="Multidensity")
        self.enmix.multifreqpoly(self.beta, xlab="Beta value")
        self.enmix.multidensity(beta1, main="Multidensity: Infinium I")
        self.enmix.multifreqpoly(beta1, main="Multidensity: Infinium I", xlab="Beta value")
        self.enmix.multidensity(beta2, main="Multidensity: Infinium II")
        self.enmix.multifreqpoly(beta2, main="Multidensity: Infinium II", xlab="Beta value")
        grdevice.dev_off()
        self.minfi.qcReport(self.RGset, pdf = "{}/qcReport.pdf".format(output_dir))
        self.minfi.mdsPlot(self.RGset)
        self.minfi.densityPlot(self.RGset, main='Beta', xlab='Beta')
Plot QC results from ENmix pipeline and possible minfi. Still experimental.

        Parameters
        ----------
        output_dir
            Where to store plots.
Plot QC results from ENmix pipeline and possible minfi. Still experimental.
Parameters

output_dir
Where to store plots.
Plot QC results from ENmix pipeline and possible minfi . Still experimental . Parameters output_dir Where to store plots .
def plot_qc_metrics(self, output_dir):
        self.enmix.plotCtrl(self.RGset)
        grdevice = importr("grDevices")
        geneplotter = importr("geneplotter")
        base = importr('base')
        anno=self.minfi.getAnnotation(self.RGset)
        anno_py = pandas2ri.ri2py(robjects.r['as'](anno,'data.frame'))
        beta_py = pandas2ri.ri2py(self.beta)
        beta1=numpy2ri.py2ri(beta_py[anno_py["Type"]=="I"])
        beta2=numpy2ri.py2ri(beta_py[anno_py["Type"]=="II"])
        grdevice.jpeg(output_dir+'/dist.jpg',height=900,width=600)
        base.par(mfrow=robjects.vectors.IntVector([3,2]))
        self.enmix.multidensity(self.beta, main="Multidensity")
        self.enmix.multifreqpoly(self.beta, xlab="Beta value")
        self.enmix.multidensity(beta1, main="Multidensity: Infinium I")
        self.enmix.multifreqpoly(beta1, main="Multidensity: Infinium I", xlab="Beta value")
        self.enmix.multidensity(beta2, main="Multidensity: Infinium II")
        self.enmix.multifreqpoly(beta2, main="Multidensity: Infinium II", xlab="Beta value")
        grdevice.dev_off()
        self.minfi.qcReport(self.RGset, pdf = "{}/qcReport.pdf".format(output_dir))
        self.minfi.mdsPlot(self.RGset)
        self.minfi.densityPlot(self.RGset, main='Beta', xlab='Beta')
def plot_qc_metrics ( self , output_dir ) : self . enmix . plotCtrl ( self . RGset ) grdevice = importr ( "grDevices" ) geneplotter = importr ( "geneplotter" ) base = importr ( 'base' ) anno = self . minfi . getAnnotation ( self . RGset ) anno_py = pandas2ri . ri2py ( robjects . r [ 'as' ] ( anno , 'data.frame' ) ) beta_py = pandas2ri . ri2py ( self . beta ) beta1 = numpy2ri . py2ri ( beta_py [ anno_py [ "Type" ] == "I" ] ) beta2 = numpy2ri . py2ri ( beta_py [ anno_py [ "Type" ] == "II" ] ) grdevice . jpeg ( output_dir + '/dist.jpg' , height = 900 , width = 600 ) base . par ( mfrow = robjects . vectors . IntVector ( [ 3 , 2 ] ) ) self . enmix . multidensity ( self . beta , main = "Multidensity" ) self . enmix . multifreqpoly ( self . beta , xlab = "Beta value" ) self . enmix . multidensity ( beta1 , main = "Multidensity: Infinium I" ) self . enmix . multifreqpoly ( beta1 , main = "Multidensity: Infinium I" , xlab = "Beta value" ) self . enmix . multidensity ( beta2 , main = "Multidensity: Infinium II" ) self . enmix . multifreqpoly ( beta2 , main = "Multidensity: Infinium II" , xlab = "Beta value" ) grdevice . dev_off ( ) self . minfi . qcReport ( self . RGset , pdf = "{}/qcReport.pdf" . format ( output_dir ) ) self . minfi . mdsPlot ( self . RGset ) self . minfi . densityPlot ( self . RGset , main = 'Beta' , xlab = 'Beta' )
Plot QC results from ENmix pipeline and possible minfi.
Plot QC results from ENmix pipeline and possible minfi .
"""Plot QC results from ENmix pipeline and possible minfi. Still experimental.

        Parameters
        ----------
        output_dir
            Where to store plots."""
self
output_dir