Comments (1)
slowkow
commented on May 23, 2024
I was able to reproduce your error.
If we look at the assignment column, we can see the issue is the presence of 5 unused categories:
[ins] In [8]: adata.obs['assignment'].value_counts().shape
Out[8]: (35,)
[ins] In [9]: (adata.obs['assignment'].value_counts() > 0).sum()
Out[9]: 30
We can use remove_unused_categories() to resolve the issue:
[ins] In [10]: adata.obs['assignment'].cat.remove_unused_categories(inplace = True)
[ins] In [11]: hm_obj = hm.run_harmony(adata.obsm['X_pca'], adata.obs, ['assignment'])
2021-05-17 10:41:38,184 - harmonypy - INFO - Iteration 1 of 10
2021-05-17 10:41:39,243 - harmonypy - INFO - Iteration 2 of 10
2021-05-17 10:41:40,278 - harmonypy - INFO - Converged after 2 iterations
from harmonypy.
Related Issues (20)
- Try filprofiler HOT 1
- How to cite this work? HOT 2
- ValueError: operands could not be broadcast together with shapes HOT 9
- Feature request: plot convergence HOT 1
- How to get the result after running harmony? HOT 2
- feature request: HOT 2
- run harmonypy true_divide error HOT 3
- Running multiple instances of the same variable in vars_use. HOT 5
- Runharmony with R and run_harmony with Python produced different results HOT 1
- Harmony with two or more covariates HOT 3
- Build changes have broken Conda install HOT 1
- Unique key is not in pandas describe HOT 3
- Add converged status to harmony object HOT 1
- Results not reproducible HOT 18
- sklearn.cluster.KMeans issue with kmeans_single() and threadpool_limits() HOT 4
- Reference mapping option HOT 2
- AttributeError: 'NoneType' object has no attribute 'split' HOT 5
- Error in running large dataset HOT 2
- Will the latest R harmony updates be propagated to the harmonypy HOT 1
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from harmonypy.