When trying to run plotpca_ScoresLoadings_plotly
(figure1.py), I'm getting the error below. I didn't change anything to this function (that I'm aware of) and I'm not familiar with this error at all. I was thinking that this may have something to do with the recent upgrade of jupyterlab to v2.0? This is not urgent so whenever you get a chance works great. Thanks.
`---------------------------------------------------------------------------
EOFError Traceback (most recent call last)
in
----> 1 plotpca_ScoresLoadings_plotly(d1.T, "AXLmuts + AF154 BR1", "AXL")
~/resistance-MS/msresist/figures/figure1.py in plotpca_ScoresLoadings_plotly(data, title, loc)
309 print(loadings.loc[loc])
310
--> 311 fig = make_subplots(rows=1, cols=2, subplot_titles=("PCA Scores", "PCA Loadings"))
312 fig.add_trace(
313 go.Scatter(
/usr/local/lib/python3.7/dist-packages/plotly/subplots.py in make_subplots(rows, cols, shared_xaxes, shared_yaxes, start_cell, print_grid, horizontal_spacing, vertical_spacing, subplot_titles, column_widths, row_heights, specs, insets, column_titles, row_titles, x_title, y_title, **kwargs)
810
811 # Build resulting figure
--> 812 fig = go.Figure(layout=layout)
813
814 # Attach subplot grid info to the figure
/usr/local/lib/python3.7/dist-packages/plotly/graph_objs/_figure.py in init(self, data, layout, frames, skip_invalid, **kwargs)
609 is invalid AND skip_invalid is False
610 """
--> 611 super(Figure, self).init(data, layout, frames, skip_invalid, **kwargs)
612
613 def add_area(
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in init(self, data, layout_plotly, frames, skip_invalid, **kwargs)
268 # --------
269 # ### Check for default template ###
--> 270 self._initialize_layout_template()
271
272 # Process kwargs
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in _initialize_layout_template(self)
1948 if self._layout_obj.template is None:
1949 if pio.templates.default is not None:
-> 1950 self._layout_obj.template = pio.templates.default
1951 else:
1952 self._layout_obj.template = None
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in setattr(self, prop, value)
4449 if match is None:
4450 # Set as ordinary property
-> 4451 super(BaseLayoutHierarchyType, self).setattr(prop, value)
4452 else:
4453 # Set as subplotid property
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in setattr(self, prop, value)
3514 if prop.startswith("_") or hasattr(self, prop) or prop in self._validators:
3515 # Let known properties and private properties through
-> 3516 super(BasePlotlyType, self).setattr(prop, value)
3517 else:
3518 # Raise error on unknown public properties
/usr/local/lib/python3.7/dist-packages/plotly/graph_objs/init.py in template(self, val)
96981 @template.setter
96982 def template(self, val):
96983 self["template"] = val
96984
96985 # ternary
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in setitem(self, prop, value)
4435 if match is None:
4436 # Set as ordinary property
-> 4437 super(BaseLayoutHierarchyType, self).setitem(prop, value)
4438 else:
4439 # Set as subplotid property
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in setitem(self, prop, value)
3480 # ### Handle compound property ###
3481 if isinstance(validator, CompoundValidator):
-> 3482 self._set_compound_prop(prop, value)
3483
3484 # ### Handle compound array property ###
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in _set_compound_prop(self, prop, val)
3834 # ------------
3835 validator = self._validators.get(prop)
-> 3836 val = validator.validate_coerce(val, skip_invalid=self._skip_invalid)
3837
3838 # Save deep copies of current and new states
/usr/local/lib/python3.7/dist-packages/_plotly_utils/basevalidators.py in validate_coerce(self, v, skip_invalid)
2714 # (could be any hashable object)
2715 if v in pio.templates:
-> 2716 return copy.deepcopy(pio.templates[v])
2717 # Otherwise, if v is a string, check to see if it consists of
2718 # multiple template names joined on '+' characters
/usr/local/lib/python3.7/dist-packages/plotly/io/_templates.py in getitem(self, item)
89 template_str = pkgutil.get_data("plotly", path).decode("utf-8")
90 template_dict = json.loads(template_str)
---> 91 template = Template(template_dict)
92
93 self._templates[template_name] = template
/usr/local/lib/python3.7/dist-packages/plotly/graph_objs/layout/init.py in init(self, arg, data, layout, **kwargs)
9448 # ----------------------------------
9449 _v = arg.pop("data", None)
-> 9450 self["data"] = data if data is not None else _v
9451 _v = arg.pop("layout", None)
9452 self["layout"] = layout if layout is not None else _v
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in setitem(self, prop, value)
3480 # ### Handle compound property ###
3481 if isinstance(validator, CompoundValidator):
-> 3482 self._set_compound_prop(prop, value)
3483
3484 # ### Handle compound array property ###
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in _set_compound_prop(self, prop, val)
3834 # ------------
3835 validator = self._validators.get(prop)
-> 3836 val = validator.validate_coerce(val, skip_invalid=self._skip_invalid)
3837
3838 # Save deep copies of current and new states
/usr/local/lib/python3.7/dist-packages/_plotly_utils/basevalidators.py in validate_coerce(self, v, skip_invalid)
2442
2443 elif isinstance(v, dict):
-> 2444 v = self.data_class(v, skip_invalid=skip_invalid)
2445
2446 elif isinstance(v, self.data_class):
/usr/local/lib/python3.7/dist-packages/plotly/graph_objs/layout/template/init.py in init(self, arg, area, barpolar, bar, box, candlestick, carpet, choroplethmapbox, choropleth, cone, contourcarpet, contour, densitymapbox, funnelarea, funnel, heatmapgl, heatmap, histogram2dcontour, histogram2d, histogram, image, indicator, isosurface, mesh3d, ohlc, parcats, parcoords, pie, pointcloud, sankey, scatter3d, scattercarpet, scattergeo, scattergl, scattermapbox, scatterpolargl, scatterpolar, scatter, scatterternary, splom, streamtube, sunburst, surface, table, treemap, violin, volume, waterfall, **kwargs)
1595 self["scattergeo"] = scattergeo if scattergeo is not None else _v
1596 _v = arg.pop("scattergl", None)
-> 1597 self["scattergl"] = scattergl if scattergl is not None else _v
1598 _v = arg.pop("scattermapbox", None)
1599 self["scattermapbox"] = scattermapbox if scattermapbox is not None else _v
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in setitem(self, prop, value)
3484 # ### Handle compound array property ###
3485 elif isinstance(validator, (CompoundArrayValidator, BaseDataValidator)):
-> 3486 self._set_array_prop(prop, value)
3487
3488 # ### Handle simple property ###
/usr/local/lib/python3.7/dist-packages/plotly/basedatatypes.py in _set_array_prop(self, prop, val)
3908 # ------------
3909 validator = self._validators.get(prop)
-> 3910 val = validator.validate_coerce(val, skip_invalid=self._skip_invalid)
3911
3912 # Save deep copies of current and new states
/usr/local/lib/python3.7/dist-packages/_plotly_utils/basevalidators.py in validate_coerce(self, v, skip_invalid)
2530 res.append(self.data_class(v_el))
2531 elif isinstance(v_el, dict):
-> 2532 res.append(self.data_class(v_el, skip_invalid=skip_invalid))
2533 else:
2534 if skip_invalid:
/usr/local/lib/python3.7/dist-packages/plotly/graph_objs/init.py in init(self, arg, connectgaps, customdata, customdatasrc, dx, dy, error_x, error_y, fill, fillcolor, hoverinfo, hoverinfosrc, hoverlabel, hovertemplate, hovertemplatesrc, hovertext, hovertextsrc, ids, idssrc, legendgroup, line, marker, meta, metasrc, mode, name, opacity, selected, selectedpoints, showlegend, stream, text, textfont, textposition, textpositionsrc, textsrc, texttemplate, texttemplatesrc, uid, uirevision, unselected, visible, x, x0, xaxis, xcalendar, xsrc, y, y0, yaxis, ycalendar, ysrc, **kwargs)
28533 # Import validators
28534 # -----------------
28535 from plotly.validators import scattergl as v_scattergl
28536
28537 # Initialize validators
/usr/lib/python3.7/importlib/_bootstrap.py in find_and_load(name, import)
/usr/lib/python3.7/importlib/_bootstrap.py in find_and_load_unlocked(name, import)
/usr/lib/python3.7/importlib/_bootstrap.py in _load_unlocked(spec)
/usr/lib/python3.7/importlib/_bootstrap_external.py in exec_module(self, module)
/usr/lib/python3.7/importlib/_bootstrap_external.py in get_code(self, fullname)
/usr/lib/python3.7/importlib/_bootstrap_external.py in _compile_bytecode(data, name, bytecode_path, source_path)
EOFError: marshal data too short`