With the current file for figure 3 the alphamap figure seems to be lacking some requirement after it installed plotly-4.12.0:
ModuleNotFoundError: No module named 'plotly.validators.histogram.marker._pattern'

Hi, julia

I send you the errors that I get when running the code

fig 4

first error in this cell of the section Read yeast go annotations downloaded from Uniprot:

yeast_go = format_uniprot_annotations(yeast_go)
yeast_go

AttributeError Traceback (most recent call last)
Cell In[13], line 1
----> 1 yeast_go = format_uniprot_annotations(yeast_go)
2 yeast_go

Cell In[9], line 32, in format_uniprot_annotations(df, sep, regex)
28 # iterate proteins
29 for e,row in df.iterrows():
30
31 # iterate annotation types
---> 32 for t,a in row.iteritems():
33 try:
34 # skip empty strings
35 if str(a) in ["", "nan"]:

File ~\anaconda3\envs\prot_vis\lib\site-packages\pandas\core\generic.py:5989, in NDFrame.getattr(self, name)
5982 if (
5983 name not in self._internal_names_set
5984 and name not in self._metadata
5985 and name not in self._accessors
5986 and self._info_axis._can_hold_identifiers_and_holds_name(name)
5987 ):
5988 return self[name]
-> 5989 return object.getattribute(self, name)

AttributeError: 'Series' object has no attribute 'iteritems'

#then i cant run all the cells linked to the output "yeast_go"

fig 5
#from this part i was able to run the code until the "radar plot" section when trynging to execute this cell...

fig_radar = px.line_polar(ap4_av_profiles.stack("Fraction").reset_index().rename({0: "value"}, axis=1),
r="value", theta="Fraction", line_group="Compartment", line_close=True,
color="Compartment", color_discrete_sequence=px.colors.qualitative.D3)
.update_layout(width=500, height=230, font_size=8, margin=dict(t=20, b=0, r=0, l=20), template="simple_white")
.update_polars(radialaxis=dict(showgrid=True, gridcolor="darkgrey"),
angularaxis=dict(showgrid=True, gridcolor="darkgrey"))
fig_radar

AttributeError Traceback (most recent call last)
Cell In[30], line 1
----> 1 fig_radar = px.line_polar(ap4_av_profiles.stack("Fraction").reset_index().rename({0: "value"}, axis=1),
2 r="value", theta="Fraction", line_group="Compartment", line_close=True,
3 color="Compartment", color_discrete_sequence=px.colors.qualitative.D3)
4 .update_layout(width=500, height=230, font_size=8, margin=dict(t=20, b=0, r=0, l=20), template="simple_white")
5 .update_polars(radialaxis=dict(showgrid=True, gridcolor="darkgrey"),
6 angularaxis=dict(showgrid=True, gridcolor="darkgrey"))
7 fig_radar

File ~\anaconda3\envs\prot_vis\lib\site-packages\pandas\core\generic.py:5989, in NDFrame.getattr(self, name)
5982 if (
5983 name not in self._internal_names_set
5984 and name not in self._metadata
5985 and name not in self._accessors
5986 and self._info_axis._can_hold_identifiers_and_holds_name(name)
5987 ):
5988 return self[name]
-> 5989 return object.getattribute(self, name)

AttributeError: 'Series' object has no attribute 'stack'

thank you

joaquin

I tried to generate figure one on my windows PC . First of all it could not find the pyRawFileReader. In the pyRawFileReader.py file line 20 I changed the path to exact path where the file is instead of getting the path by os.path.dirname(os.path.abspath(file)) and also I added this to the utils.py before line "from pyrawfilereader import RawFileReader":

import sys
sys.path.append('Actual Jupyter notebook path)

By this way I think I managed to run pyRawFileReader but again I have this error :

ext\utils.py:163, in check_sanity(mass_list)
156 def check_sanity(
157 mass_list
...
--> 163 mass_list[0][i] <= mass_list[0][i + 1] for i in range(len(mass_list[0]) - 1)
164 ):
165 raise ValueError("Masses are not sorted.")

IndexError: list index out of range

it seems the reading file is empty. Also I downloaded the rawfile that was default for your analysis and it gave me same error. so the problem is not raw file. I don't know what else I can do