I am currently trying to generate a heatmap in python from a text file, using R commands (with rpy2). It works fine in R, but when I take it to python, the Quartz interface displays quickly and then closes. I would like either to be able to save the quartz display to a file, or directly save my heatmap to a file without displaying it.
Here is the code I have been using:
import rpy2.robjects as robjects
robjects.r('''
library("gplots")
data = read.csv("/Users/.../Heatmap_data.txt")
DF = data.frame(data)
MD = data.matrix(DF,rownames.force=NA)
heatmap.2(MD, scale="none", col=redgreen(100), cexRow=0.1, key=FALSE, symkey=FALSE, trace="none", Colv=FALSE)
''')
I'm using python 2.7, on OS X Yosemite. Thank you for any help.
import numpy as np
import rpy2.robjects as ro
import rpy2.robjects.numpy2ri
ro.numpy2ri.activate()
R = ro.r
data = np.random.random((10, 10))
R.png(file='/tmp/out.png')
R.heatmap(data)
R("dev.off()")
writes to the file /tmp/out.png
without displaying the image:
.
Preventing the displayed image from immediately closing can be done like this:
script.py:
import numpy as np
import rpy2.robjects as ro
import rpy2.robjects.numpy2ri
import rpy2.rinterface as rinterface
import time
import threading
ro.numpy2ri.activate()
R = ro.r
def ion():
def r_refresh(interval = 0.03):
while True:
rinterface.process_revents()
time.sleep(interval)
t = threading.Thread(target=r_refresh)
t.daemon = True
t.start()
ion()
data = np.random.random((10, 10))
R.heatmap(data)
R("dev.copy(png,'/tmp/out2.png')")
R("dev.off()")
try:
# for Python2
raw_input()
except NameError:
# for Python3
input()
The raw_input
or input
call prevents the Python interpreter from exiting, thus allowing the window to stay open, until the user presses Enter.
The ion
function calls rinterface.process_revents()
periodically so the displayed window will react to GUI events such as resizing or being closed.
dev.copy(png,'/tmp/out2.png')
saves the already-displayed image to a file .
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