topometry

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First off thank you so much for the great package and manuscript. It's awesome to see such important work done in dimensionality reduction/single cell unifying and comparing the DR methods....

hoangthienan95

When to consider using TopOMetry over UMAP?

2

I think some people (myself included) will come across this method being familiar with UMAP and classical dimensionality reduction techniques, but it might not be clear when to use UMAP...

sgbaird

I'm getting an error when trying to run this bit of code in Colab: ``` import topo as tp tg = tp.TopOGraph() tg.run_layouts(emb, n_components=2, bases=['diffusion', 'fuzzy'], graphs=['diff', 'fuzzy'], layouts=['MAP', 'PaCMAP'])...

rxjx

hey davi, thanks for the great tool, I just started diving into looking into my data using the evaluation functions. Just wanted to point out that the trustworthniness function in...

daniel-spies

Hi, I have recently started to play with single cell data analysis and your biorxiv paper and approach sounds really interesting. I understand how PCA dimensional reduction is probably the...

jdmontenegro

comparing classic umap and topometry

2

sorry if my question is naive but its for better understanding 1-in a classical workflow, if i use Topometry, is the eigncomponents here considered the dimensionality reduction method? 2- for...

Marwansha

Map projection looks odd with high number of cells

1

Sorry for Bothering again, but after testing on my entire dataset not just 1 sample, around 3/4 million cell, i observe this MAP projection and am not sure what could...

Marwansha

paCMAP generate an error ,

1

using same code with MAP projecion works fine > projections=["MAP"] `tg = tp.TopOGraph(n_eigs=119, n_jobs=-1, verbosity=0) tg.run_models(adata.X, kernels=['bw_adaptive'], eigenmap_methods=['msDM'], projections=["PaCMAP"]) --------------------------------------------------------------------------- ValueError Traceback (most recent call last) Cell In[65], line 3...

Marwansha