Matching coordinates to cell names

[alicerlam]

Hi!

I'm trying to export coordinate data to be able to display/work with them in Python, but coordinates.txt contains numbered cells without rownames. The numbers do not seem to match the order of the rownames of the matrix I input into SPRING (assigning them likewise and plotting results in substantially different graphs than seen in the SPRING viewer). Is there any way to know which cell in the original matrix each coordinate corresponds to? Thanks!

[calebweinreb]

Hi Alice,

By default, SPRING performs total-counts filtering of cells before generating the plot. Unfortunately there is no way for the user to download an explicit index of which cells were filtered, so that would prevent matching up the coordinates with the original rows of your input matrix. (I definitely should have included this option... not sure why we didn't).

So the best that can be done in your case is to perform cell filtering yourself before uploading the data to SPRING, and then setting the minimum number of counts to 0 when generating the plot so that no other cells get filtered. Then (assuming you do not make any "subplots"), the rows of the downloaded coordinates file should match up one-to-one with the rows of the uploaded gene expression matrix.