Comments (2)
biopzhang
commented on July 30, 2024
3
I had similar problem here.
My set up is:
MacOS Ventura
Python==3.9.16, rpy2==3.5.11, anndata2ri==1.2
tradeSeq 1.10.0, R version 4.2.2
I made a couple of changes in the tools/_downstream_analysis.py and it worked. Feel free to access my modified one (https://github.com/biopzhang/COMMOT/blob/main/commot/tools/_downstream_analysis.py). If @zcang is interested, please investigate and consider to incorporate it to the repo. Nonetheless, I'm not a huge fan of rpy2, I would rather consider to directly run the R code in R environment and read the outputs from python (which is also painful) ...
from commot.
ccruizm
commented on July 30, 2024
Hello @bernard2012, could you figure this out? Also trying to implement commot+tradeseq but have faced the same problems 😕
from commot.
Related Issues (20)
- Questions about dis_thr
- Comparing cell-type-level communication scores across samples HOT 2
- Please refer to 'igraph' instead of 'python-igraph'
- legend and image store in two separate files
- Questions about the meaning of arrow lengths HOT 1
- Question about the COMMOT paper HOT 1
- Module 'commot' has no attribute 'pp'
- Questions about slow running time
- Crop and zoom into the sample for `plot_cell_communication`
- Usage of cell2location results in COMMOT for spatial interaction
- orientation of images in cell_communication output HOT 2
- How does commot calculates distance on visium data
- Why do you solve 4-dimensional matrix `P` in four problems?
- error' single positional indexer is out-of-bounds' when using 'ct.tl.spatial_communication' HOT 1
- COMMOT in Seurat object
- How does commot calculates the number of L-R HOT 3
- Updated the requirements.txt
- when I run“import commot as ct”，there is something wrong
- TypeError: _detect_vcs() missing 2 required positional arguments: 'expected_vcs' and 'path' 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 commot.