R script to Python conversion

[bvk]

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.

[dpryan]

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

[bvk]

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 !!

[bvk]

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 ?

[dpryan]

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

[bvk]

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

[dpryan]

You'll want to use Rscript rather than R.

[bvk]

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'])

[dpryan]

Yup, something like that should work for you

[bvk]

Yup, something like that should work for you

Thankyou