UMAP (Uniform Manifold Approximation and Projection) is a novel manifold manifold learning technique for dimension reduction. The UMAP algorithm is competitive with t-SNE for visualization quality and arguably preserves more of the global structure and superior run time performance. UMAP has not computational restrictions on embedding dimensions making it viable as a general purpose dimension reduction technique for machine learning
Questions tagged [runumap]
38 questions
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How to perform Weighted dimensionality reduction with Umap
The title pretty much says it all, I have a df with 40+ dimension which I'd like to process into the Umap algorithm in order to have a 2-d output.
I would like to know if it is possible to weight the input columns differently for the purpose of…
Luca
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What do r_orig and r_emb parameters represent in UMAP algorithm?
What do exactly rad_orig and r_emb represent in umap.UMAP? (docs).
These parameters are available when output_dens flag is set.
Reading the docs:
r_orig: array, shape (n_samples)
Local radii of data points in the original data…
James Arten
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'what' must be a function or character string in R error message
I am plotting different umaps.
I have a part of the code that worked yesterday, however today I get the error message: Error in do.call(c, lapply(2:ncol(nn_idx), function(i) as.vector(rbind(nn_idx[, : 'what' must be a function or character…
George
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How to fix UMAP layout?
I am trying to use UMAP through umap-learn. And I am running 2,000,000 cells with 16 dimensions as my training dataset and another 1,000,000 cells with 16 dimensions as my testing dataset. However, when I add another 100,000 cells to my testing…
rachelyyyqq
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UMAP not working on Jupyter (thru Anaconda)
I'm trying to use UMAP in Jupyter (on Anaconda's environment) but something is not working properly. Below is the code I used.
# INSTALL UMAP
conda install -c conda-forge umap-learn # this was what was mentioned on umap's website
import…
Lucy
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My mac doesn't show seaborn plot without error message?
In [14]: import seaborn as sns
...: import matplotlib.pyplot as plt
...:
...: l = [41, 44, 46, 46, 47, 47, 48, 48, 49, 51, 52, 53, 53, 53, 53, 55, 55, 55,
...: 55, 56, 56, 56, 56, 56, 56, 57, 57, 57, 57, 57, 57, 57, 57, 58, 58,…
marlon
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Can I save the coordinates for a UMAP embedding?
I am running a UMAP model as follows:
embedding = umap.UMAP(n_components=2,n_neighbors=30, min_dist=0.0, metric='euclidean').fit(data)
And plotting:
f = umap.plot.points(embedding, labels=df['name'])
This generates a nice looking graph.…
fdgnhgdh
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umap highlighting two different models
I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap plot showing the different clusters but I want to show where the ptx samples and human samples are.
My code is as follows:
#create the Seurat…
mmpp
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