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  • R script to Python conversion

    setwd("/pipeline/deff")
    source('http://www.bioconductor.org/biocLite.R')
    biocLite('cummeRbund')
    library(cummeRbund)
    cuff_data <- readCufflinks('deff')
    pdf("allplots.pdf")
    #"distbtn of expression levels for each dataset"
    plot(csDensity(genes(cuff_data)))
    #"compare the exp of each gene in all the conditions with scatter plot"
    plot(csScatterMatrix(genes(cuff_data)))
    #"distances between condition with dendrogram"
    plot(csDendro(genes(cuff_data)))
    #"to inspect differentially expressed genes"
    plot(csVolcanoMatrix(genes(cuff_data)))
    dev.off()

    Can anyone help how to write a python script for plotting cuffdiff output.

  • #2
    Why reinvent the wheel? R is a perfectly adequate language for tasks like this. Just call an Rscript from python if you need to.

    Comment


    • #3
      Originally posted by dpryan View Post
      Why reinvent the wheel? R is a perfectly adequate language for tasks like this. Just call an Rscript from python if you need to.
      Yes, but I just want to give a try with python. Anyways I'l use R only. Thank you !!

      Comment


      • #4
        Originally posted by dpryan View Post
        Why reinvent the wheel? R is a perfectly adequate language for tasks like this. Just call an Rscript from python if you need to.
        How to call an R script from python ?

        Comment


        • #5
          The subprocess module would be a common method to call any other functions from within python.

          Comment


          • #6
            Originally posted by dpryan View Post
            The subprocess module would be a common method to call any other functions from within python.
            import subprocess
            retcode = subprocess.call(['/usr/bin/R','/path/to/analysis.R'])

            Is this enough to call my analysis.R script

            Comment


            • #7
              You'll want to use Rscript rather than R.

              Comment


              • #8
                Originally posted by dpryan View Post
                You'll want to use Rscript rather than R.
                Ok. So

                import subprocess
                retcode = subprocess.call(['/usr/bin/Rscript','/san/gh/ngs/con/analysis.R'])

                Comment


                • #9
                  Yup, something like that should work for you

                  Comment


                  • #10
                    Originally posted by dpryan View Post
                    Yup, something like that should work for you
                    Thankyou

                    Comment

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