TypeError: Dimensions of C (100, 50) are incompatible with X (51) and/or Y (100); see help(pcolormesh)

[pna059]

Hi,
I am processing HiC-Pro (iced, split by chromosome) output to call TADs.
The tadtool tads work, but I don`t know how to determine the parameters without plot function.
However, i keep getting this error when using tadtool plot:

tadtool/bin/tadtool plot leaf_20000_iced_chr1H.matrix leaf_20000_iced_chr1H_abs.bed chr1H:1-1000000
[sudo] password for pavla: 
2022-08-05 08:58:40,039 INFO Loading regions...
2022-08-05 08:58:40,111 INFO Checking plotting region in matrix...
2022-08-05 08:58:40,111 INFO Loading matrix...
2022-08-05 08:59:14,519 INFO Getting window sizes...
2022-08-05 08:59:14,600 INFO Calculating index...
100% (100 of 100) |###################################################################################| Elapsed Time: 0:06:35 Time:  0:06:35
2022-08-05 09:05:51,284 INFO Done. Showing plot...
/usr/local/lib/python3.10/dist-packages/numpy-1.23.1-py3.10-linux-x86_64.egg/numpy/lib/function_base.py:4691: UserWarning: Warning: 'partition' will ignore the 'mask' of the MaskedArray.
  arr.partition(
Traceback (most recent call last):
  File "/home/pavla/Documents/Barley_HiC/Tadtool/tadtool/bin/tadtool", line 448, in <module>
    TADtool()
  File "/home/pavla/Documents/Barley_HiC/Tadtool/tadtool/bin/tadtool", line 44, in __init__
    getattr(self, args.command)()
  File "/home/pavla/Documents/Barley_HiC/Tadtool/tadtool/bin/tadtool", line 207, in plot
    fig, axes = tad_plot.plot(plotting_region)
  File "/usr/local/lib/python3.10/dist-packages/tadtool-0.82-py3.10.egg/tadtool/plot.py", line 677, in plot
  File "/usr/local/lib/python3.10/dist-packages/tadtool-0.82-py3.10.egg/tadtool/plot.py", line 202, in plot
  File "/usr/local/lib/python3.10/dist-packages/tadtool-0.82-py3.10.egg/tadtool/plot.py", line 357, in _plot
  File "/usr/local/lib/python3.10/dist-packages/matplotlib-3.5.2-py3.10-linux-x86_64.egg/matplotlib/__init__.py", line 1412, in inner
    return func(ax, *map(sanitize_sequence, args), **kwargs)
  File "/usr/local/lib/python3.10/dist-packages/matplotlib-3.5.2-py3.10-linux-x86_64.egg/matplotlib/axes/_axes.py", line 6058, in pcolormesh
    X, Y, C, shading = self._pcolorargs('pcolormesh', *args,
  File "/usr/local/lib/python3.10/dist-packages/matplotlib-3.5.2-py3.10-linux-x86_64.egg/matplotlib/axes/_axes.py", line 5568, in _pcolorargs
    raise TypeError('Dimensions of C %s are incompatible with'
TypeError: Dimensions of C (100, 50) are incompatible with X (51) and/or Y (100); see help(pcolormesh)

The two input files look like this:

head leaf_20000_iced_chr1H_abs.bed 
chr1H	0	20000	1
chr1H	20000	40000	2
chr1H	40000	60000	3
chr1H	60000	80000	4
chr1H	80000	100000	5
chr1H	100000	120000	6
chr1H	120000	140000	7
chr1H	140000	160000	8
chr1H	160000	180000	9
chr1H	180000	200000	10

head leaf_20000_iced_chr1H.matrix
2	2	29.285
2	3	38.969
2	4	20.755
2	5	13.023
2	6	5.271
2	7	2.195
2	8	7.402
2	9	0.626
2	10	2.692
2	11	3.763

What can I do to make it working?

Thank you!

[porpheria]

Hello,
I am also having the same error, while using the tadtool plot.
Is there any update regarding this ?

[kaukrise]

Thanks for reminding me of this. Please try version 0.83 from Pypi

pip install tadtool==0.83

[porpheria]

Thank you for your quick reply.
tadtool plot is working now. Thanks once again.

[porpheria]

Hello again,
I am facing another issue for tadtool plot.
While using the -w option for providing the custom window size, I am having this below error.
"ValueError: Cannot load file containing pickled data when allow_pickle=False".
I was providing a text file with two window size, 100000 and 200000, separated by space.
Thank you in advance.

[kaukrise]

Can you please post the complete error? It contains valuable information for debugging.

[porpheria]

Below is the command I used and the error,

porpheria$ tadtool plot siCon_Un_Rep2n3_chr1.matrix siCon_Un_Rep2n3_chr1_abs.bed chr1:30500000-40500000 -n 248956422 -w WindowSize.txt
2022-11-15 14:30:12,677 INFO Loading regions...
2022-11-15 14:30:12,767 INFO Checking plotting region in matrix...
2022-11-15 14:30:12,768 INFO Loading matrix...
2022-11-15 14:30:17,598 INFO Getting window sizes...
Traceback (most recent call last):
File "/Users/porpheria/miniconda3/envs/Tadtool/bin/tadtool", line 448, in
TADtool()
File "/Users/porpheria/miniconda3/envs/Tadtool/bin/tadtool", line 44, in init
getattr(self, args.command)()
File "/Users/porpheria/miniconda3/envs/Tadtool/bin/tadtool", line 163, in plot
window_sizes = np.load(args.window_sizes[0])
File "/Users/porpheria/miniconda3/envs/Tadtool/lib/python3.9/site-packages/numpy/lib/npyio.py", line 418, in load
raise ValueError("Cannot load file containing pickled data "
ValueError: Cannot load file containing pickled data when allow_pickle=False

[kaukrise]

Thanks for bringing this to my attention, it seems as though numpy changed one of the exception types. I uploaded version 0.84, which should work with window size files again.

[porpheria]

Thank you Kaukrise,
It's working fine withe window size file.