Comments (3)
Yes it does work. Easy way to test, take some cells out from a cell type and remap. Also, you can map using cluster mode (which takes all cells of a certain cell types and compute the average, so you are actually mapping one cell per cell type).
from tangram.
Thanks for your reply. I did a similar experiment (Copy all cells of modality M1 to M2. To simulate the ratio mismatch, cells of cell type A in the M1 modality were a subset of A in M2 by random reasmpling. Finally, cells were mapped from data modality M1 to M2). However, I got a very different mapping result of the original mapping without resampling and the mapping with resampling, either for the cell or cluster mode. Also, if I analyze this problem theoretically, I do not think I can get the same results either. Since the cells in M2 were copied from original M1, I know the ideal mapping matrix. Then, if I calculate the feature expression of M2 based on M1 with the ideal mapping matrix for the two mappings (resamped and original) separately, their cosine similarities in the loss function can be different.
Based on the above, I think the ratio of celltypes may influence the mapping results. If I am wrong, please correct me. Thank you so much!
from tangram.
That's interesting. I would love to see a figure to understand how much this matters.
Tangram look for a minimum of a loss function. If you change cell type ratio (aside from the fact that you are removing single cells, ie puzzle pieces, that could affect mapping quality), it should not change "too much" in the sense that the same minimum should still be there, given that a single cell can be used several times. However, it may be harder for Tangram to reach that minimum, and may converge on a different, less good one.
Cool!
from tangram.
Related Issues (20)
- Can we have an API as batch size for the integration method? HOT 3
- No attribute 'pp_adatas' in tangram HOT 2
- Possible to use multiple single cell datasets in Tangram? HOT 3
- Cannot find correspondence of the input data HOT 1
- question about training genes HOT 1
- Some questions about best practices HOT 1
- Attribute error : module 'tangram' has no attribute 'map_cells_to_space' HOT 2
- scRNAseq cells < spatial cells, curious about how mapping works HOT 3
- Unexpected behaviour HOT 1
- Question about acceptable AUC, improving AUC HOT 1
- potential overfitting HOT 5
- Interpretation of tangram_ct_pred HOT 2
- Option "enforce gene lowercase" HOT 1
- error when sq.im.segment
- Tangram Deconvolution HOT 1
- Using Integrated single cell data for alignment
- AttributeError: module 'tangram' has no attribute 'pp_adatas'
- Sparsity_sc and sparsity_sp = 0
- Please explain `project_cell_annotations`
- Projecting spatial annotations to single cell HOT 2
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 tangram.