Tkinter GUI for R Scripts: How to streamline Tkinter file input into an R script to run on button click

Question

I am building a toolbox for bioinformatical analysis of DNA sequences. All the statistical analysis is done in R. I have written the R scripts for these.

I am now building a GUI with Tkinter so users can choose a file with DNA information and run my R scripts on them. I am at the very beginning of the Tkinter script and I am stuck on getting the information (directory path) the user selects into my R script, which is then executed on that file.

Here is the test code if you want to run the GUI yourself:

import Tkinter
import tkMessageBox
import tkFileDialog
import os
import sys
import subprocess

top = Tkinter.Tk()
CDR3Merge = "PHB_forR.R"

#####----------Definitions------------####

#Definition to open file browser and select file.
def FileOpen():
    var.set(tkFileDialog.askopenfilename(defaultextension=".txt"))

#Definition to start R-Script
def CDR3Extract():
    os.popen("R CMD BATCH PHB_forR.R").read()


####----------Buttons and their Functions-------------####

#Button to browse and open/select file
ButtonOpenFile = Tkinter.Button(top, text="Open File", command = FileOpen)
ButtonOpenFile.grid(row=1, column=1)

#Button to Execute R-Script
ButtonCDR3Extract = Tkinter.Button(top, text="CDR3 Extraction", command = CDR3Extract)
ButtonCDR3Extract.grid(row=2,column=0)

#####----------Entry Bars and their Definition--------####
#Label at the very top
TopLabel = Tkinter.Label(text="CDR3 Extraction")
TopLabel.grid(row=0, column=0)

#Entry for file selection
var = Tkinter.StringVar()
FileEntry = Tkinter.Entry(top, width=60, textvariable= var)
FileEntry.grid(row=1,column=0)


####---------------------------------------------------####

top.mainloop()

And Im guessing we need to focus on this part:

  #Definition to open file browser and select file.
def FileOpen():
    var.set(tkFileDialog.askopenfilename(defaultextension=".txt"))

#Definition to start R-Script
def CDR3Extract():
    os.popen("R CMD BATCH PHB_forR.R").read()

I don´t know if it is necessary to post my R script, but the method/code with which I read my .txt file in R is following:

read.delim("file.txt",header=TRUE, sep="\t")

How can I turn the output of the askopenfile command from Tkinter into a variable used in my R script? Is this even possible or should I consider a different method of doing this?

Thank you.

Edit: After Dason recommended to check out commandArgs() in R I wanted to print the filepath together with the command to run the Rscript. So now the button CDR3 Extract will do folliwng:

def CDR3Extract():
        os.popen("Rscript PHB_forR.R" + " " + str(var).read()

var still being

var = Tkinter.SrtingVar()

The problem I am having now is that var is returned as PY_VAR0 instead of the filepath that is printed in my entry box.

I have tried var.get() and using that but it also returns as PY_VAR0.

Any suggestions? I am probably looking at this the wrong way I can´t find or come up with something more simple.

Thank you! I think I'm almost there, I have set up the R script to use as commandArgs() so when I execute Rscript PHB_forR.R filename.Rit will use filename.R as the file to read. However, this does not seem to work with the file in a different directory as the script and neither have I been able to get the path of the file into the definition/command in my python script. I thought os.popen("R CMD BATCH PHB_forR.R", var).read()would do it, as var is the path directory, however I get a error message that says TypeError: must be string, not instance" — Vaxin
– Vaxin, Commented Dec 12, 2015 at 21:02

Vaxin · Accepted Answer · 2015-12-13 15:32:10Z

Alright so here is what works:

def CDR3Extract():
os.popen("Rscript test_forR.R" + " " + var.get()).read()

as varis set to return the file path selected by the user it had to be added as var.get(). This way it does not return as PY_VAR0 but as the path. To recap how varis set:

def FileOpen():
    var.set(tkFileDialog.askopenfilename(defaultextension=".txt"))
var = Tkinter.StringVar()

Running Rscript script.R /path/to/file.txtworks, however, in order to get only the filepath when using commandArgs()I had to get rid of script.Rin R, because commandArgs()would give me:

filepath <- commandArgs()
filepath
[1] script.R
[2] /path/to/file.txt

so I used

filepath2 <- filepath[-1]
filepath2
[1] /path/to/file.txt

The file can then be read in R with

read.delim(filepath2,header=TRUE, sep="\t")

I hope I answered the question in a way outsiders can follow? Please let me know if I should go into more detail.

Thank you for your help.

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