I am trying to run single-cell analysis on scanpy 1.9.1. When I try to run scanpy.pl.umap(adata, color=["PDGFRB","RGS5"], s = 30), I get the following error:
TypeError Traceback (most recent call last)
in
----> 1 sc.pl.umap(adata, color=["PDGFRB","RGS5"], s = 30)
5 frames
/usr/local/lib/python3.8/dist-packages/matplotlib/colorbar.py in init(self, ax, mappable, **kw)
1228 """
1229 Return colorbar data coordinates for the boundaries of
-> 1230 a proportional colorbar, plus extension lengths if required:
1231 """
1232 if (isinstance(self.norm, colors.BoundaryNorm) or
TypeError: init() got an unexpected keyword argument 'location'
And I get a blank color heat legend.
blank_color_heat_legend
I saw someone suggested using an older version of matplotlib for a similar problem. This error occurred in matplotlib 3.6.3, so I tried installing matplotlib 3.1.3 but it did not work either.
Any help will be appreciated!
Related
When executing the below
profile = ProfileReport(df,title="Data Profile Report")
profile.to_file("data_profile_report.html")
Here is the exception thrown
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
c:\Projections 2022-08-16\Projections.py in <cell line: 4>()
102 # %%
103 #Creating EDA of data
104 profile = ProfileReport(df_cdap,title="CDAP Data Profile Report")
----> 105 profile.to_file("cdap_data_profile_report.html")
File c:\Users\fengq\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas_profiling\profile_report.py:257, in ProfileReport.to_file(self, output_file, silent)
254 self.config.html.assets_prefix = str(output_file.stem) + "_assets"
255 create_html_assets(self.config, output_file)
--> 257 data = self.to_html()
259 if output_file.suffix != ".html":
260 suffix = output_file.suffix
File c:\Users\fengq\AppData\Local\Programs\Python\Python39\lib\site-packages\pandas_profiling\profile_report.py:368, in ProfileReport.to_html(self)
360 def to_html(self) -> str:
361 """Generate and return complete template as lengthy string
362 for using with frameworks.
363
(...)
366
367 """
--> 368 return self.html
...
--> 810 fig = manager.canvas.figure
811 if fig_label:
812 fig.set_label(fig_label)
AttributeError: 'NoneType' object has no attribute 'canvas'
I've tried to re-install python and reinstalling the dependencies for pandas-profiling but nothing seems to work so far. I've also tried downgrading python to python 3.9 and the matplotlib to an older version as well. It has not changed this error.
I notice that the error seems to be attributed to "manager.canvas.figure" but I'm not sure how to resolve it from that point onwards. Any help is greatly appreciated!
The problem resolved as I set the matplotlib to inline as per some comments that I was able to find on another forum. I'm still really interested to learn what causes this! Please feel free to answer and suggest other solutions! I would love to try them!
I'm trying to simulate the segregation process in a city for a school project. I've managed to plot the city when initialized and after segregation, but I don't manage to create the animation showing the city's inhabitants moving to show the evolution.
I have two methods in my Ville class (I'm coding in French) that should make the animation together.
def afficher(self, inclure_satisfaction=False, inclure_carte_categories=False, size=5):
carte = self.carte_categories(inclure_satisfaction=inclure_satisfaction)
if inclure_carte_categories:
print("Voici la carte des catégories (à titre de vérification)")
print(carte)
mat_rs = masked_array(carte, carte!=1.5)
mat_ri = masked_array(carte, carte!=1)
mat_bs = masked_array(carte, carte!=2.5)
mat_bi = masked_array(carte, carte!=2)
plt.figure(figsize=(size, size))
affichage_rs = plt.imshow(mat_rs, cmap=cmap_rs)
affichage_ri = plt.imshow(mat_ri, cmap=cmap_ri)
affichage_bs = plt.imshow(mat_bs, cmap=cmap_bs)
affichage_bi = plt.imshow(mat_bi, cmap=cmap_bi)
return plt.figure()
(this function plot the map by first getting an array from the method carte_categories in function of the category of each inhabitant and then getting an array for each value to plot)
def resoudre2(self):
fig = plt.figure(figsize=(5,5))
list_of_artists = []
while self.habitants_insatisfaits != []:
self.demenagement_insatisfait_aleatoire()
list_of_artists.append([self.afficher(inclure_satisfaction=True)])
ani = ArtistAnimation(fig, list_of_artists, interval=200, blit=True)
return ani
(habitants_insatisfaits is a list that contains the "insatisfied inhabitants": there are two few people of their category around them, so they want to move somewhere else; so resoudre means solve, and this function loops until all the inhabitants are satisfied where they are (and this way the society is mechanically segregated)
The initialized city looks like this initialized city (dark colors for insatisfied inhabitants), and the segregated city looks like that segregated city.
But when I enter
a = ville1.resoudre2(compter=True)
I don't get an animation but only this error message:
/usr/local/lib/python3.7/dist-packages/ipykernel_launcher.py:211: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
/usr/local/lib/python3.7/dist-packages/ipykernel_launcher.py:206: RuntimeWarning: More than 20 figures have been opened. Figures created through the pyplot interface (`matplotlib.pyplot.figure`) are retained until explicitly closed and may consume too much memory. (To control this warning, see the rcParam `figure.max_open_warning`).
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/matplotlib/cbook/__init__.py", line 196, in process
func(*args, **kwargs)
File "/usr/local/lib/python3.7/dist-packages/matplotlib/animation.py", line 951, in _start
self._init_draw()
File "/usr/local/lib/python3.7/dist-packages/matplotlib/animation.py", line 1533, in _init_draw
fig.canvas.draw_idle()
AttributeError: 'NoneType' object has no attribute 'canvas'
/usr/local/lib/python3.7/dist-packages/matplotlib/image.py:452: UserWarning: Warning: converting a masked element to nan.
dv = np.float64(self.norm.vmax) - np.float64(self.norm.vmin)
/usr/local/lib/python3.7/dist-packages/matplotlib/image.py:459: UserWarning: Warning: converting a masked element to nan.
a_min = np.float64(newmin)
/usr/local/lib/python3.7/dist-packages/matplotlib/image.py:464: UserWarning: Warning: converting a masked element to nan.
a_max = np.float64(newmax)
<string>:6: UserWarning: Warning: converting a masked element to nan.
/usr/local/lib/python3.7/dist-packages/matplotlib/colors.py:993: UserWarning: Warning: converting a masked element to nan.
data = np.asarray(value)
(first problem) and then every map (corresponding to each step of the segregating city) is plotted (second problem; see here). And when I try to type
print(a)
from IPython.display import HTML
HTML(a.to_html5_video())
to plot the animation, I only get
<matplotlib.animation.ArtistAnimation object at 0x7f4cd376bfd0>
---------------------------------------------------------------------------
AttributeError Traceback (most recent call last)
<ipython-input-20-d7ca1fcdadb6> in <module>()
1 print(a)
2 from IPython.display import HTML
----> 3 HTML(a.to_html5_video())
2 frames
/usr/local/lib/python3.7/dist-packages/matplotlib/animation.py in _init_draw(self)
1531 # Flush the needed figures
1532 for fig in figs:
-> 1533 fig.canvas.draw_idle()
1534
1535 def _pre_draw(self, framedata, blit):
AttributeError: 'NoneType' object has no attribute 'canvas'
So I don't understand why I get this error and not just my animation...
Thank you for your help, it's the first time I ask questions here so don't hesitate if you need more details about my code! :)
Nathan
Had the same issue, downgrading Matplotlib fixed the issue for me.
pip install matplotlib==3.5.1
I'm trying to write a scraper to scrape Option prices from Yahoo Finance. The code below is working and even gives the correct output answer. The problem is that right before the answer, I get the following error:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
~/anaconda3/lib/python3.7/site-packages/IPython/core/formatters.py in __call__(self, obj)
343 method = get_real_method(obj, self.print_method)
344 if method is not None:
--> 345 return method()
346 return None
347 else:
~/anaconda3/lib/python3.7/site-packages/pandas/core/frame.py in _repr_html_(self)
694 See Also
695 --------
--> 696 to_html : Convert DataFrame to HTML.
697
698 Examples
~/anaconda3/lib/python3.7/site-packages/pandas/core/frame.py in to_html(self, buf, columns, col_space, header, index, na_rep, formatters, float_format, sparsify, index_names, justify, bold_rows, classes, escape, max_rows, max_cols, show_dimensions, notebook, decimal, border, table_id)
2035 Dictionary mapping columns containing datetime types to stata
2036 internal format to use when writing the dates. Options are 'tc',
-> 2037 'td', 'tm', 'tw', 'th', 'tq', 'ty'. Column can be either an integer
2038 or a name. Datetime columns that do not have a conversion type
2039 specified will be converted to 'tc'. Raises NotImplementedError if
~/anaconda3/lib/python3.7/site-packages/pandas/io/formats/format.py in to_html(self, classes, notebook, border)
751 need_leadsp = dict(zip(fmt_columns, map(is_numeric_dtype, dtypes)))
752
--> 753 def space_format(x, y):
754 if (y not in self.formatters and
755 need_leadsp[x] and not restrict_formatting):
TypeError: __init__() got an unexpected keyword argument 'max_rows'
I tried researching the cause of the error in different stackoverflow questions, as well as the github repo of the pandas library. The closest thing I found was in the what's new section of the pandas 0.24.0 "max_rows and max_cols parameters removed from HTMLFormatter since truncation is handled by DataFrameFormatter GH23818"
My code is as follows:
import lxml
import requests
from time import sleep
ticker = 'AAPL'
url = "http://finance.yahoo.com/quote/%s/options?p=%s"%(ticker,ticker)
response = requests.get(url, verify=False)
print ("Parsing %s"%(url))
sleep(15)
parser = lxml.html.fromstring(response.text)
tables = parser.xpath('//table')
print(len(tables))
puts = lxml.etree.tostring(tables[1], method='html')
df = pd.read_html(puts, flavor='bs4')[0]
df.tail()
The df.tail() shows correctly the last 5 rows of the table, but I can't seem to remove the error. Also every time I use the dataframe, I get a correct result, but the error is shown again.
Thanks in advance in helping with my error.
For future reference:
The error was driven by the anaconda install of the packages.
By pip installing the packages, the error goes away.
BR
I am trying the following:
After downloading http://eric.clst.org/assets/wiki/uploads/Stuff/gz_2010_us_050_00_20m.json
In [2]: import geopandas
In [3]: geopandas.read_file('./gz_2010_us_050_00_20m.json')
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-3-83a1d4a0fc1f> in <module>
----> 1 geopandas.read_file('./gz_2010_us_050_00_20m.json')
~/miniconda3/envs/ml3/lib/python3.6/site-packages/geopandas/io/file.py in read_file(filename, **kwargs)
24 else:
25 f_filt = f
---> 26 gdf = GeoDataFrame.from_features(f_filt, crs=crs)
27
28 # re-order with column order from metadata, with geometry last
~/miniconda3/envs/ml3/lib/python3.6/site-packages/geopandas/geodataframe.py in from_features(cls, features, crs)
207
208 rows = []
--> 209 for f in features_lst:
210 if hasattr(f, "__geo_interface__"):
211 f = f.__geo_interface__
fiona/ogrext.pyx in fiona.ogrext.Iterator.__next__()
fiona/ogrext.pyx in fiona.ogrext.FeatureBuilder.build()
TypeError: startswith first arg must be bytes or a tuple of bytes, not str
On the page http://eric.clst.org/tech/usgeojson/ with 4 geojson files under the 20m column, the above file corresponds to the US Counties row, and is the only one that cannot be read out of the 4. The error message isn't very informative, I wonder what's the reason, please?
If your error message looks anything like "Polygons and MultiPolygons should follow the right-hand rule", it means the order of the coordinates in those GeoObjects should be clock-wise.
Here's an online tool to "fix" your objects, with a short explanation:
https://mapster.me/right-hand-rule-geojson-fixer/
Possibly an answer for people arriving at this page, I received the same error and the error was thrown due to encoding issues.
Try encoding the initial file with utf-8 or try opening the file with an encoding which you think is applied to the file. This fixed my error.
More info here
Had a quick question regarding a pandas DataFrame and the pd.read_pickle() function. Basically, I have a large but simple Dataframe (333 mb). When I run pd.read_pickle on the dataframe, I am getting and EOFError.
Is there any way around this issue? What might be causing this?
I saw the same EOFError when I created a pickle using:
pandas.DataFrame.to_pickle('path.pkl', compression='bz2')
and then tried to read with:
pandas.read_pickle('path.pkl')
I fixed the issue by supplying the compression on read:
pandas.read_pickle('path.pkl', compression='bz2')
According to the Pandas docs:
compression : {‘infer’, ‘gzip’, ‘bz2’, ‘zip’, ‘xz’, None}, default ‘infer’
string representing the compression to use in the output file. By default,
infers from the file extension in specified path.
Thus, simply changing the path from 'path.pkl' to 'path.bz2' also fixed the problem.
I can confirm the valuable comment of greg_data:
When I encountered this error I worked out that it was due to the
initial pickling not having completed correctly. The pickle file was
created, but not finished correctly. Seems to me this is the only
possible source of the EOFError in pickle, that the pickle is
malformed, i.e. not finished.
My error during pickling was:
---------------------------------------------------------------------------
TypeError Traceback (most recent call last)
<ipython-input-40-263240bbee7e> in <module>()
----> 1 main()
<ipython-input-38-9b3c6d782a2a> in main()
43 with open("/content/drive/MyDrive/{}.file".format(tm.id), "wb") as f:
---> 44 pickle.dump(tm, f, pickle.HIGHEST_PROTOCOL)
45
46 print('Coherence:', get_coherence(tm, token_lists, 'c_v'))
TypeError: can't pickle weakref objects
And when reading that pickle file that was obviously not finished during pickling, the reported error occured:
pd.read_pickle(r'/content/drive/MyDrive/TEST_2021_06_01_10_23_02.file')
Error:
---------------------------------------------------------------------------
EOFError Traceback (most recent call last)
<ipython-input-41-460bdd0a2779> in <module>()
----> 1 object = pd.read_pickle(r'/content/drive/MyDrive/TEST_2021_06_01_10_23_02.file')
/usr/local/lib/python3.7/dist-packages/pandas/io/pickle.py in read_pickle(filepath_or_buffer, compression)
180 # We want to silence any warnings about, e.g. moved modules.
181 warnings.simplefilter("ignore", Warning)
--> 182 return pickle.load(f)
183 except excs_to_catch:
184 # e.g.
EOFError: Ran out of input