Comments (11)
What version of scanpy do you use?
from conos.
I'm using scanpy ver. 1.4.3
from conos.
It was indeed an issue with the scanpy version. After downgrading to ver. 1.4.1 I was able to proceed with the analysis.
from conos.
I have the same issue.
Please, Can I know how I could downgrade version of Scanpy to 1.4.1?
from conos.
It was indeed an issue with the scanpy version. After downgrading to ver. 1.4.1 I was able to proceed with the analysis.
I have the same issue.
Please, Can I know how I could downgrade version of Scanpy to 1.4.1?
from conos.
Yeah, I need to get in contact with scanpy folks to fix this issue.
@DuaaAlawad , see comment to #33
from conos.
Yeah, I need to get in contact with scanpy folks to fix this issue.
@DuaaAlawad , see comment to #33
thanks .. I got the solution.
pip install scanpy==1.4.1
from conos.
Hey! Scanpy uses the umap
function to find approximate knn graphs. This looks like it has something to do with the newest umap
update, which was incorporated into scanpy. Maybe @ivirshup could give some insight into this?
from conos.
Thanks for the ping, I think I see the issue.
We try and get the parameters used to create the neighbor network so that we can make sure we're computing the UMAP layout on the right data, using the right methods. This requires a few parameters:
- To make sure we're using the right data, we need the representation the neighbors were calculated on, so the values of
use_rep
andn_pcs
. - UMAP needs to know the distance metric that was used for some cases of the layout. This would be passed as a string for the key
metric
. If it's a metric which takes additional arguments those would be passed in a dict undermetric_kwds
.
On the scanpy end of things, we could make it so your call doesn't throw an error by just assuming you used default values, but I don't think that would be a good idea. I would suggest providing those parameters when you add the neighbor graph to the AnnData
object.
Here's the relevant code from scanpy: https://github.com/theislab/scanpy/blob/d8f32c040f3a5f4fc07998b269796ca58de84b40/scanpy/tools/_umap.py#L128-L150
from conos.
Thank you so much, @ivirshup ! Updated it in e7f2f37, now everything works fine.
from conos.
This fix seems to have been removed again in #45
from conos.
Related Issues (20)
- Passing Leiden or Walktrap clusters to plotDEheatmap HOT 5
- Redundant Suggests after transfer to sccore HOT 1
- Wrong legend while using custom palette HOT 3
- Downsample from each cluster HOT 3
- Cell subsetting error HOT 4
- docker build fails HOT 1
- 'adjustedRand not in load table' HOT 6
- conos install error igraph.so not found HOT 16
- getDifferentialGenes for selected groups? HOT 6
- shared NN variant of $buildGraph HOT 5
- findSubcommunities HOT 7
- Rstudio session crash when making Conos object (LeidenAlg cluster estimation) HOT 11
- Running Conos functions across multiple nodes/computers HOT 1
- How to get predicted cell types? HOT 2
- why I can't find the "velocityInfoConos" function in conos(v1.4.6)? HOT 5
- largeVis embedding does not utilize n.cores argument HOT 5
- Feeding output from getPerCellTypeDE into Heatmap HOT 2
- Integration of multi-modal data based on a joint space
- Prepare for upcoming Seurat v5 release HOT 1
- Attaching metadata from Seurat Objects 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 conos.