dms-vep / dms-vep-pipeline-3

Pipeline for analyzing deep mutational scanning (DMS) of viral entry proteins (VEPs)
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Potential package version conflict with dmslogo? #74

Closed Caleb-Carr closed 1 year ago

Caleb-Carr commented 1 year ago

When using the dms-vep-pipeline-3 conda environment and trying to run the minimal dmslogo example below, the following error occurs:

dmslogo code:

data = pd.DataFrame.from_records(
        data=   [(    1,      'A',        1),
                 (    1,      'C',      0.7),
                 (    2,      'C',      0.1),
                 (    2,      'D',      1.2),
                 (    5,      'A',      0.4),
                 (    5,      'K',      0.4)],
        columns=['site', 'letter', 'height'])

data

fig, ax = dmslogo.draw_logo(data=data,
                            x_col='site',
                            letter_col='letter',
                            letter_height_col='height')

Error:

     73 def draw_path(self, renderer, gc, tpath, affine, rgbFace):
     74     """Draw the letters."""
---> 75     affine = affine.identity().scale(self._sx, self._sy) + affine
     76     renderer.draw_path(gc, tpath, affine, rgbFace)

AttributeError: 'Affine2D' object has no attribute 'identity'
jbloom commented 1 year ago

Probably related to this:

transforms.Affine2D.identity()
... is removed in favor of directly calling the [Affine2D](https://matplotlib.org/stable/api/transformations.html#matplotlib.transforms.Affine2D) constructor with no arguments.
jbloom commented 1 year ago

@Caleb-Carr. this is fixed in dmslogo 0.7.0, which is now incorporated into dms-vep-pipeline-3 version 3.4.9.