some error when Plot the genome-wide map at 40000kb resolution

[xiaorenwu1111]

Professor,
I met some error when I plot the genome-wide map at 40000kb resolution.Could you help me?
[@n-1-29 HiCPlotter-0.6.6]$ python HiCPlotter.py -f /data3/users/HiC/Mus_musculus/GSM862720_results/hic_results/matrix/GSM862720/iced/40000/GSM862720_40000_iced.matrix -o GSM862720 -r 40000 -tri 1 -bed /data3/users/HiC/Mus_musculus/GSM862720_results/hic_results/matrix/GSM862720/raw/40000/GSM862720_40000_abs.bed -n hES -wg 1 -chr chrX
Plotting now!!
Traceback (most recent call last):
File "HiCPlotter.py", line 1715, in
HiCplotter(**args)
File "HiCPlotter.py", line 1556, in HiCplotter
plt.savefig(output+'-WholeGenome-'+str(resolution/1000)+'K'+extension,dpi=200)
File "/data/users//miniconda3/lib/python2.7/site-packages/matplotlib/pyplot.py", line 697, in savefig
res = fig.savefig(*args, **kwargs)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/figure.py", line 1573, in savefig
self.canvas.print_figure(*args, **kwargs)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/backend_bases.py", line 2252, in print_figure
**kwargs)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 545, in print_png
FigureCanvasAgg.draw(self)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/backends/backend_agg.py", line 464, in draw
self.figure.draw(self.renderer)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/figure.py", line 1144, in draw
renderer, self, dsu, self.suppressComposite)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
a.draw(renderer)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/axes/_base.py", line 2426, in draw
mimage._draw_list_compositing_images(renderer, self, dsu)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/image.py", line 139, in _draw_list_compositing_images
a.draw(renderer)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/artist.py", line 63, in draw_wrapper
draw(artist, renderer, *args, **kwargs)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/image.py", line 543, in draw
renderer, renderer.get_image_magnification())
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/image.py", line 770, in make_image
unsampled=unsampled)
File "/data/users/miniconda3/lib/python2.7/site-packages/matplotlib/image.py", line 373, in _make_image
rgba = np.empty((A.shape[0], A.shape[1], 4), dtype=A.dtype)
MemoryError

[akdemirlab]

Hi,
I think the issue here is that your matrix becomes too big and your computer's memory is not enough for plotting it. Tbh, plotting whole genome data with 40kb resolution will not give you much detail. I would plot whole genome matrix with the 1MB resolution first and then you can try to plot individual chromosomes with a 40kb resolution. I hope this helps...