Comments (5)
@michalk8 please !
from cellrank.
Can you please print the kernel ctk
? How did you initialize it?
from cellrank.
from cellrank.kernels import CytoTRACEKernel
ctk = CytoTRACEKernel(adata).compute_cytotrace()
ctk return to Nonetype
when ctk = CytoTRACEKernel(adata)
return to
and ctk.compute_transition_matrix(threshold_scheme="soft", nu=0.5) runs successfully
but when i run ctk.plot_projection(basis="umap", color="celltype", legend_loc="right")
AttributeError Traceback (most recent call last)
Input In [35], in <cell line: 1>()
----> 1 ctk.plot_projection(basis="umap", color="celltype", legend_loc="right")
AttributeError: 'CytoTRACEKernel' object has no attribute 'plot_projection'
from cellrank.
Hi @fanjiacheng-max , can you please post the full code snippet + output of the following:
import cellrank as cr
print(cr.__version__)
ctk = ... # run your code
print(type(ctk), dir(ctk))
from cellrank.
Closing this due to inactivity.
from cellrank.
Related Issues (20)
- Fix linting
- cr.pl.gene_trends() gives empty plots HOT 3
- `g.plot_fate_probabilities` fails for `same_plot=False` HOT 1
- Update documentation to include CellRank 2 preprint
- Inconsistent `time_key` types between `RealTimeKernel.from_moscot()` and `TemporalProblem.prepare()` HOT 2
- AttributeError with cr.pl.gene.trends HOT 3
- Pseudotime differences HOT 2
- estimators.GPCCA.plot_macrostates() gives error for legend plotting HOT 7
- AttributeError: 'GPCCA' object has no attribute 'compute_fate_probabilities' HOT 2
- vk has no attribute plot_projection? HOT 7
- vk.plot_projection(): KeyError: "Unable to find a basis in `adata.obsm['X_umap']` or `adata.obsm['umap']`." HOT 2
- Estimating Fate Probabilities and Driver Genes----Uncover driver genes: RuntimeError: No stationary distribution found in `.eigendecomposition['stationary_dist']`. HOT 4
- Identify states -> I get ValueError: Sparse implementation is only available for `method='krylov'`. HOT 3
- How to delete gridlines in figures HOT 2
- Request for Intestinal organoid dataset(scEU-seq) HOT 3
- Setting of vk.plot_projection() HOT 2
- ValueError: setting an array element with a sequence HOT 4
- P-value for cellrank.pl.log_odds HOT 2
- Tolerance not exposed 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 cellrank.