Copy link Author . It is essential to align the values of the operations which require the unique index values with the index. 1058 # a 1 Also, be aware that the .obs_names need to be the same in the two AnnData. 3784 if not self._index_as_unique and len(indexer): What is known about the homotopy type of the classifier of subobjects of simplicial sets? If there are duplicate labels, an exception Its preserved through Currently, many methods fail to 4483 fill_value=fill_value. reindex? Your Go-To Resource for Learn & Build: CSS,JavaScript,HTML,PHP,C++ and MYSQL. it is expected that every method taking or returning one or more # File /pandas/pandas/core/flags.py:105, in Flags.__setitem__(self, key, value) Remove Duplicated indexes. To see all available qualifiers, see our documentation. 4670 ) from ctgan import CTGANSynthesizer, discrete_columns = [ Let me know if this solution fixes the problem for now at least. 4105 # trying to reindex on an axis with duplicates 1354 return obs, var Apparently, the python error is the result of doing operations on a DataFrame that has duplicate index values. # By clicking Accept all cookies, you agree Stack Exchange can store cookies on your device and disclose information in accordance with our Cookie Policy. OverflowAI: Where Community & AI Come Together, "ValueError: cannot reindex from a duplicate axis", Behind the scenes with the folks building OverflowAI (Ep. # 4670 ) # Can a lightweight cyclist climb better than the heavier one by producing less power? Check your email for magic link to sign-in. The ValueError: cannot reindex on an axis with duplicate labels error occurs when you try to reindex a pandas dataframe with duplicate labels. # 5085 errors=errors, By executing this code. 1464 element=element. # X [0, 2] Can you try again with installing from source? ~/anaconda3/envs/sc-tutorial/lib/python3.7/site-packages/pandas/core/generic.py in _reindex_with_indexers(self, reindexers, fill_value, copy, allow_dups) # 4990 labels, level=level, limit=limit, tolerance=tolerance, method=method Can you have ChatGPT 4 "explain" how it generated an answer? raise ValueError ("cannot reindex on an axis with duplicate labels") ValueError: cannot reindex on an axis with duplicate labels I have tried removing the duplicated timestamps for each symbol: df = df.groupby ( ['symbol', 'timestamp']) df = df.last ().sort_index ().reset_index () 247079 // before 233228 // after But it still gives the same error ~/anaconda3/envs/sc-tutorial/lib/python3.7/site-packages/pandas/core/series.py in getitem(self, key) # positions I just reinstalled from source. DataFrame that disallows duplicates will raise an 4491 You see valueerror: cannot reindex from a duplicate axis because of an operation that holds value of a duplicate index. Below is the method you will use to check for the duplicate values. # 5079 index=index, pandas? # 4598 axis = self._get_axis_number(axis) 1928 # if it's worth supporting that. # 5049 copy = False 1506 """ 1927 # setting for extensionarrays that store dicts. # () If you need additional logic to handle duplicate labels, rather than just 4354 # perform the reindex on the axes # 713 msg += f"\n{duplicates}" Already on GitHub? --> 136 _adata._inplace_subset_var(common_vars) Have a question about this project? Would be grateful to hear whether this is still buggy. # # 0 2 3287 # trying to reindex on an axis with duplicates ----> 2 scv.utils.merge(adata, adata_velocity), ~/anaconda3/envs/sc-tutorial/lib/python3.7/site-packages/scvelo/read_load.py in merge(adata, ldata, copy) Built with the PyData Sphinx Theme 0.13.3. # 91 for ax in obj.axes: # -> 4601 return super()._rename( The version of seaborn is 0.11.2 # DuplicateLabelError: Index has duplicates. Some pandas methods (Series.reindex() for example) just dont work with The error in python looks like this: It is widespread to see such an error in Panda, but Panda also helps you to clean up the messy data. How to convert mouse gene_id to Entrez gene ids General tingxie2020 August 20, 2022, 2:48am 1 Hi, I used the following code to get biomart gene annotation for my mouse genes: annot = sc.queries.biomart_annotations ( "mmusculus", ["ensembl_gene_id", "entrez_gene_id","start_position", "end_position", "chromosome_name"], NaN value in Panda means a missing number. 1055 orig = self.plot_data[var].dropna() You can use the duplicated() method to identify the duplicate labels in your dataframe. # File /pandas/pandas/core/generic.py:5040, in NDFrame._reindex_with_indexers(self, reindexers, fill_value, copy, allow_dups) "ValueError: cannot reindex on an axis with duplicate labels". # 5550 # For subclasses using _metadata. ValueError: cannot reindex from a duplicate axis - Net-Informations.Com adata.var_names_make_unique() Duplicated() can also remove or prevent duplicate values for you. Then you have to find the columns for the DataFrame. errors.DuplicateLabelError. replaced the real values with something else to hide sensitive information) - Korem Dec 1, 2014 at 20:12 @Korem, I don't think this is true, but even if this is true, why would this cause the above error? SQL, you know that row labels are similar to a primary key on a table, and you This method will return a value in a boolean. # How to convert mouse gene_id to Entrez gene ids - scverse Why do code answers tend to be given in Python when no language is specified in the prompt? -> 4356 fill_value, copy).finalize(self) The Journey of an Electromagnetic Wave Exiting a Router, Previous owner used an Excessive number of wall anchors, Align \vdots at the center of an `aligned` environment. How do I select rows from a DataFrame based on column values? 4398 def reindex(self, index=None, **kwargs): If you look at the error message " cannot reindex from a duplicate axis ", it means that Pandas DataFrame has duplicate index values. Connect and share knowledge within a single location that is structured and easy to search. ","acceptedAnswer":{"@type":"Answer","text":"NaN value in Panda means a missing number. NaN stands for Not a Number, which is how a missing value in Panda is commonly represented. 'sudden weight loss', This is also encountered in the following casehttps://medium.com/analytics-vidhya/a-step-by-step-guide-to-generate-tabular-synthetic-dataset-with-gans-d55fc373c8db. # File /pandas/pandas/core/generic.py:5549, in NDFrame.__finalize__(self, other, method, **kwargs) If youre familiar with Fortunately, there are several ways to fix this error. # 681 if axis >= self.ndim: You've successfully signed in. (internally in), # File /pandas/pandas/core/indexes/base.py:715, in Index._maybe_check_unique(self) If we slice 'B', we get back a Series. This error can happen when you try to append or concatenate two dataframes that have overlapping index labels. To find the data frames index, you can use the method named get_loc(). 909 key = check_bool_indexer(self.index, key) # 5000 # If we've made a copy once, no need to make another one messy, real-world data before it goes to some downstream system. File ~/work/pandas/pandas/pandas/core/generic.py:5538, (self, axes, level, limit, tolerance, method, fill_value, copy). (i.e. If you're familiar with SQL, you know that row labels are similar to a primary key on a table, and you would never want duplicates in a SQL table. rev2023.7.27.43548. - Akavall Dec 1, 2014 at 21:10 6 ValueError: cannot reindex from a duplicate axis - Stack Overflow # 5547 self.attrs[name] = other.attrs[name] 4674 @deprecate_nonkeyword_arguments(version=None, allowed_args=["self", "labels"]), ~/anaconda3/envs/gan/lib/python3.8/site-packages/pandas/core/generic.py in reindex(self, *args, **kwargs) # 4971 return self._reindex_multi(axes, copy, fill_value) DataFrame. Hence, you need to apply all the methods we have discussed above to the columns if you want to avoid getting the same error in your code. 402 if common_bins: ~/anaconda3/envs/gan/lib/python3.8/site-packages/seaborn/_core.py in comp_data(self) @peterson7773702 @chenh38 1 adata_velocity = scv.read('/home/ec2-user/velocyto/aggregate.loom', cache=False) 1277 5033 index, # This section describes how duplicate labels change the behavior of certain 714 'Irritability', https://www.kaggle.com/uciml/pima-indians-diabetes-database?select=diabetes.csv, I am using pandas 1.1.3 and table-evaluator 1.3.?. 3786 2022 Position Is Everything All right reserved. Assumed that you have your Timestamp as index to begin with, you need to do the resample first, and reset_index before doing a groupby, here's the working sample: As said in comment, your 'Timestamp' isn't datetime and probably as string so you cannot resample by DatetimeIndex, just reset_index and convert it something like this: Now just run the previous code again but replace 'Timestamp' with 'ts' and you should be OK. 1791 # if it's worth supporting that. You can find the index by following the methods given above and correct the problem by keeping the code stated earlier as an example. 3736 @appender(generic.NDFrame.reindex.doc) Seriesindex(3)NaN, indexValueError: cannot reindex from a duplicate axis, labelindex'a', index'a''a', pandasreindex() Is there a better way to do this? 1460 if p.univariate: # --> 679 self.axes[axis]._validate_can_reindex(indexer) Your program cannot execute until the values given in the code are not aligned with the values of the operations that require unique index values. , pandasissue ValueError: cannot reindex from a duplicate axis, pandas -> 3785 raise ValueError("cannot reindex from a duplicate axis") # 5046 copy=copy, If you are already sure there must be duplicate values but need to know how to find those values; You can use the duplicated method. 1374 4523 # TODO: speed up on homogeneous DataFrame objects # a 0 data 4373 fill_value=fill_value, For example, well resolve duplicates by taking the average of all rows So if you try to reindex a Dataframe, join with another Dataframe or resample a Dataframe, it will not work. I have come across the same problem, got exactly the error line "_core.py:1057: FutureWarning: reindexing " . Remember that the default values in the new index created, which are not present in the DataFrame, are assigned NaN.
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