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Didn't know the user had run the analysis, added location of coordinates.
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Kohl Kinning
Kohl Kinning
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Cell Ranger

To answer the first point of your question: No. You can't download the tSNE coordinates for cells directly from the Analysis tab of the fancy, polished .html document that Cell Ranger produces. If you have access to the machine on which the pipeline was run, you can grab the intermediate files. Everything is well documented by 10X. They explain defaults etc. on that page. The tSNE coordinates are available at:

analysis/tsne/2_components/projection.csv

and the contents look like:

$ head -5 analysis/tsne/2_components/projection.csv
Barcode,TSNE-1,TSNE-2
AAACATACAACGAA-1,-13.5494,1.4674
AAACATACTACGCA-1,-2.7325,-10.6347
AAACCGTGTCTCGC-1,12.9590,-1.6369
AAACGCACAACCAC-1,-9.3585,-6.7300

Seurat

And the second point: Cell Ranger is replicating the Seurat workflow. Seurat uses the Louvain method for community detection by default. Check out the intro tutorial and see if you can follow along. This tutorial works with 10X data, in fact the first function call in the tutorial reads in the 10X matrices. If you are already plotting in R you'll speed through this tutorial. Seurat is great to work with, you'll have tSNEs and clusters in no time. And there's so much more you can do from there!

Cell Ranger

To answer the first point of your question: No. You can't download the tSNE coordinates for cells directly from the Analysis tab of the fancy, polished .html document that Cell Ranger produces.

Seurat

And the second point: Cell Ranger is replicating the Seurat workflow. Seurat uses the Louvain method for community detection by default. Check out the intro tutorial and see if you can follow along. This tutorial works with 10X data, in fact the first function call in the tutorial reads in the 10X matrices. If you are already plotting in R you'll speed through this tutorial. Seurat is great to work with, you'll have tSNEs and clusters in no time. And there's so much more you can do from there!

Cell Ranger

You can't download the tSNE coordinates for cells directly from the Analysis tab of the fancy, polished .html document that Cell Ranger produces. If you have access to the machine on which the pipeline was run, you can grab the intermediate files. Everything is well documented by 10X. They explain defaults etc. on that page. The tSNE coordinates are available at:

analysis/tsne/2_components/projection.csv

and the contents look like:

$ head -5 analysis/tsne/2_components/projection.csv
Barcode,TSNE-1,TSNE-2
AAACATACAACGAA-1,-13.5494,1.4674
AAACATACTACGCA-1,-2.7325,-10.6347
AAACCGTGTCTCGC-1,12.9590,-1.6369
AAACGCACAACCAC-1,-9.3585,-6.7300

Seurat

And the second point: Cell Ranger is replicating the Seurat workflow. Seurat uses the Louvain method for community detection by default. Check out the intro tutorial and see if you can follow along. This tutorial works with 10X data, in fact the first function call in the tutorial reads in the 10X matrices. If you are already plotting in R you'll speed through this tutorial. Seurat is great to work with, you'll have tSNEs and clusters in no time. And there's so much more you can do from there!

Source Link
Kohl Kinning
Kohl Kinning
  • 1.1k
  • 6
  • 27

Cell Ranger

To answer the first point of your question: No. You can't download the tSNE coordinates for cells directly from the Analysis tab of the fancy, polished .html document that Cell Ranger produces.

Seurat

And the second point: Cell Ranger is replicating the Seurat workflow. Seurat uses the Louvain method for community detection by default. Check out the intro tutorial and see if you can follow along. This tutorial works with 10X data, in fact the first function call in the tutorial reads in the 10X matrices. If you are already plotting in R you'll speed through this tutorial. Seurat is great to work with, you'll have tSNEs and clusters in no time. And there's so much more you can do from there!