Problem with `region` in `fanc/bin/fancplot`
kalavattam opened this issue · 3 comments
kalavattam commented
Hi,
Thank you for the great program, which I'm in the midst of learning to use. I'm trying to plot an .mcool file. I am running the following command:
#!/bin/bash
f_Q=08_zoom/MC-2019_Q_WT_repM.standard-rDNA-complete.mcool
res=6400
fancplot \
-o "test.png" \
XII:100000-200000 \
-p square \
--title "6400 bp, XII:100000-200000" \
--colormap "germany" \
"${f_Q}@${res}"I am getting the following error message, which I'm finding difficult to troubleshoot:
/home/kalavatt/miniconda3/envs/fanc_env/bin/fancplot:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('fanc==0.9.26')
2023-09-29 12:52:47,947 INFO Using non-interactive backend
2023-09-29 12:52:48,324 INFO Found 1 regions
/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/bin/fancplot:187: UserWarning: There was an error with plot 0, region XII:100000-200000 (Traceback (most recent call last):
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/bin/fancplot", line 170, in __init__
fig, axes = gf.plot(plot_region)
^^^^^^^^^^^^^^^^^^^^
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/plotter.py", line 211, in plot
p.plot(r)
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 786, in plot
self._after_plot((x_region, y_region))
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 581, in _after_plot
self.add_colorbar()
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 651, in add_colorbar
self.update_colorbar(vmin=self.vmin, vmax=self.vmax, baseline=baseline)
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 669, in update_colorbar
self.colorbar.draw_all()
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Colorbar' object has no attribute 'draw_all'
)
warnings.warn("There was an error with plot {}, region {}:{}-{} ({})".format(i, region.chromosome,
2023-09-29 12:52:48,514 WARNING 'Colorbar' object has no attribute 'draw_all'I see that this is associated with these portion of code:
- https://github.com/vaquerizaslab/fanc/blob/main/bin/fancplot#L187
- https://github.com/vaquerizaslab/fanc/blob/main/fanc/plotting/plotter.py#L211
- https://github.com/vaquerizaslab/fanc/blob/main/fanc/plotting/base_plotter.py#L786
- https://github.com/vaquerizaslab/fanc/blob/main/fanc/plotting/base_plotter.py#L581
- https://github.com/vaquerizaslab/fanc/blob/main/fanc/plotting/base_plotter.py#L651
- https://github.com/vaquerizaslab/fanc/blob/main/fanc/plotting/base_plotter.py#L669
The file is for Hi-C from S. cerevisiae, which have chromosomes with roman-numeral names. I can confirm that the chromosome name "XII" is correct and the regions 100000–200000 exist and contain data. I can also confirm that the resolution 6400 exists in the .mcool.
Do you have any advice on troubleshooting this? Thanks.
–Kris
kalavattam commented
Specifying vmin, vmax, and a matplotlib color (with argument -c) results in the same error:
#!/bin/bash
fancplot \
-o "test.pdf" \
XII:100000-200000 \
-p square \
-vmin 0 -vmax 0.1 \
--title "6400 bp, XII:100000-200000" \
-c Reds \
08_zoom/MC-2019_Q_WT_repM.standard-rDNA-complete.mcool@6400/home/kalavatt/miniconda3/envs/fanc_env/bin/fancplot:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
__import__('pkg_resources').require('fanc==0.9.26')
2023-09-29 13:14:42,151 INFO Using non-interactive backend
2023-09-29 13:14:42,582 INFO Found 1 regions
/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/bin/fancplot:187: UserWarning: There was an error with plot 0, region XII:100000-200000 (Traceback (most recent call last):
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/bin/fancplot", line 170, in __init__
fig, axes = gf.plot(plot_region)
^^^^^^^^^^^^^^^^^^^^
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/plotter.py", line 211, in plot
p.plot(r)
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 786, in plot
self._after_plot((x_region, y_region))
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 581, in _after_plot
self.add_colorbar()
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 651, in add_colorbar
self.update_colorbar(vmin=self.vmin, vmax=self.vmax, baseline=baseline)
File "/fh/fast/tsukiyama_t/grp/tsukiyamalab/kalavatt/2023_rDNA/src/fanc/fanc/plotting/base_plotter.py", line 669, in update_colorbar
self.colorbar.draw_all()
^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Colorbar' object has no attribute 'draw_all'
)
warnings.warn("There was an error with plot {}, region {}:{}-{} ({})".format(i, region.chromosome,
2023-09-29 13:14:42,775 WARNING 'Colorbar' object has no attribute 'draw_all'kaukrise commented
This should be fixed in the latest available version, 0.9.27
kalavattam commented
Thank you—updating from 0.9.26 (pip install of git clone http://www.github.com/vaquerizaslab/fanc) to 0.9.27 (pip install of file posted here) resolved the issue. Closing now.