Comments (5)
Yes, it can work with any matrix! I won't make any guarantees about how long it takes, though. If you preprocess your matrix, be sure to disable normalization (--normalization NoneNorm
) and filterings (--no-filter
). If taking too long from the dense matrix, try it out with the sparse matrix without PCA, it might worth it.
from too-many-cells.
As an update to this, I did not account for negative abundances. However, I have switched to using a signed Laplacian for the spectral clustering which should resolve this issue. Otherwise, the NaNs (from the inverse square root of the negatives) would have led to SVDLIBC hanging. For instance, I ran too-many-cells
on your PCA data and it was taking forever. Switching to signed Laplacian now has it take literally a second. I will re-open this issue until I release a new version with a new docker. I should note that I have not altered the modularity calculation.
from too-many-cells.
Solved in GregorySchwartz/spectral-clustering@12175d1 and in too-many-cells-0.1.1.0
. Waiting for docker.
from too-many-cells.
Docker version uploaded to https://cloud.docker.com/repository/docker/gregoryschwartz/too-many-cells/general. This version includes --dense
to use BLAS/LAPACK for clustering. May be faster for dense matrices.
from too-many-cells.
However, I have switched to using a signed Laplacian for the spectral clustering which should resolve this issue. Otherwise, the NaNs (from the inverse square root of the negatives) would have led to SVDLIBC hanging.
Thanks for the update! That explains why it didn't make any progress running for hours on 32 CPUs... Now it works really fast!
There still seems to be a minor issue though (see #3).
from too-many-cells.
Related Issues (20)
- kent-394 not supported HOT 9
- Running a million cells failed in the docker HOT 2
- Purity section in too-many-cells HOT 4
- error, called at src/Data/Sparse/SpMatrix.hs:793:22 in sparse-linear-algebra-0.3.2-LJ5QWDyWqk8g1L9MLmVBX:Data.Sparse.SpMatrix HOT 5
- comparative analysis of clustering performance HOT 2
- comparative analysis of clustering performance #37 HOT 3
- can't install the included projects HOT 13
- Error when installing with nix on CentOS 7 HOT 4
- Strange warnings occurred during the procedure HOT 3
- A problem for batch effect removed data HOT 11
- fail when downloading ucsc browser HOT 2
- The pipeline crashed with error message HOT 3
- Index out of bounds for TooManyPeaks HOT 7
- Prune parameters setting question HOT 1
- Question: Does well separated color in the dendrogram mean that the items are distinct? HOT 1
- Seurat SCtransform HOT 1
- Installation fails with nix-env ('__noChroot' set, but that's not allowed when 'sandbox' is 'true') HOT 7
- How to modify the colors of the PieChart HOT 1
- Expected runtime HOT 1
- Is matrixValidity printing row and column wrong? HOT 17
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from too-many-cells.