Comments (5)
I think that I figured it out. I found a conflict between "slingshot" with another library that was attached in my environment. The library is "cerebroApp" (https://github.com/romanhaa/Cerebro). It is used also for trajectory analysis and interactive visualization of scRNA-seq data. I tested the SlingshotDataSet() function with and witout this library, and it's definitely what was causing the problem: SlingshotDataSet() works perfectly when "cerebroApp" is not attched, and fails with this weird error message when it's attached. Now, "cerebroApp" imports and suggests no less than 39 other libraries! I did not have time to test which is causing the conflict, but if someone is willing to do the testing, I'd be happy to learn about it. Also, "cerebroApp" is no longer supported. So, it may be a good idea to stay away from it when using "slingshot". Any suggestion is welcome. Thanks.
from slingshot.
Hi @jedazard,
I looked into this a little bit and I'm not sure where the error is coming from. As far as I can tell, nothing in slingshot
uses as(, "dgCMatrix")
, so this must be something that gets called from another package. I'll keep an eye out for this error, though, in case it pops up again and will try to update this thread if I figure out what's causing it. For now, I think your solution of avoiding having both packages loaded at the same time is probably the best one.
Best,
Kelly
from slingshot.
Dear Kelly,
i came across the same error with @jedazard
As i was using the function lines(SlingshotDataSet(ss), lwd=2, col='black')
The R outputs as follows: Error: as(<dsCMatrix>, "dgCMatrix") is deprecated since Matrix 1.5-0; do as(., "generalMatrix") instead
But I did not library the"cerebroApp" like @jedazard said.
I guess some dependencies had updated their function. Could you find the solution about it , thanks very much!
from slingshot.
Hi @peanut-123,
Thanks for reporting this! I'm not able to reproduce this error, unfortunately, so is there any chance you could send me some code causes it?
Thanks,
Kelly
from slingshot.
Related Issues (20)
- Trajectories with multiple starting clusters HOT 7
- Installing Slingshot with R version 4.0.5 HOT 2
- trajectory bootstrapping and uncertainty HOT 3
- Slingshot pseudotime with CellRank HOT 8
- error when trying to overlay the lineage trajectory on umap HOT 2
- Slingshot curves look weird HOT 2
- Trajectory over condtions not ending in center HOT 1
- steps you have to take after slingshot HOT 1
- one question about psuedo time inference HOT 1
- pseudotime distribution is uneven when run slingshot on a subset of dimensionality reduction HOT 6
- What assay to use after Seurat integration HOT 2
- Error plotting the trajectory HOT 2
- Clustering discrepancy with Slingshot and Seurat HOT 5
- Porting slingshot to Python HOT 4
- Calculating cell weights HOT 4
- Scale or not to scale the genes by their variance in real datasets HOT 2
- the cluster in end.clust is not the end of pseudotime value HOT 4
- Running Multiple Times Results In Some Cells Not Plotting HOT 3
- How to plot the pseudotime for all lineages together in one UMAP plot? HOT 3
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 slingshot.