Failure to plot logos when using pdf renderer
Closed this issue · 1 comments
blaiseli commented
- pyseqlogo version: commit bda975f
- Python version: Python 3.7.9
- Operating System: MX Linux 17 (Debian-based distribution)
Description
I wanted to try draw_logo from within an automated pipeline, where, for some reason, I had to set a pdf renderer for matplotlib, and draw_logo crashed on line 127 of pyseqlogo.py:
126 window_ext = txt.get_window_extent(
--> 127 txt._renderer) #(fig.canvas.renderer) #txt._renderer)
What I Did
Here is a minimum example to reproduce the crash:
>>> import matplotlib as mpl
>>> mpl.use("PDF")
>>> from pyseqlogo.pyseqlogo import draw_logo
>>> data = {"A": [5, 5, 5, 5], "C": [5, 5, 5, 5], "G": [5, 5, 5, 5], "T": [5, 5, 5, 5]}
>>> fig, axes = draw_logo(data, data_type="counts")
RuntimeError Traceback (most recent call last)
<ipython-input-5-5a59f0cf5a0b> in <module>
----> 1 fig, axes = draw_logo(data, data_type="counts")
/usr/local/lib/python3.7/site-packages/pyseqlogo/pyseqlogo.py in draw_logo(data, data_type, seq_type, yaxis, colorscheme, nrow, ncol, padding, draw_range, coordinate_type, draw_axis, fontfamily, debug, ax)
364 else:
365 xshifts_list = _draw_text_data_coord(
--> 366 ic, ax, fontfamily, colorscheme, draw_axis=draw_axis)
367 else:
368 if yaxis == 'probability':
/usr/local/lib/python3.7/site-packages/pyseqlogo/pyseqlogo.py in _draw_text_data_coord(height_matrix, ax, fontfamily, colorscheme, scalex, draw_axis, debug)
125 fig.canvas.draw()
126 window_ext = txt.get_window_extent(
--> 127 txt._renderer) #(fig.canvas.renderer) #txt._renderer)
128 if basescore > 0.3:
129 yshift = window_ext.height * basescore #- fontsize/10# fontsize/4#/1.20 #*.85 #* fig.dpi/72.0
/usr/local/lib/python3.7/site-packages/matplotlib/text.py in get_window_extent(self, renderer, dpi)
895 self._renderer = self.figure._cachedRenderer
896 if self._renderer is None:
--> 897 raise RuntimeError('Cannot get window extent w/o renderer')
898
899 with cbook._setattr_cm(self.figure, dpi=dpi):
RuntimeError: Cannot get window extent w/o renderer