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JEFworks-Lab / STdeconvolve

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data
http://jef.works/STdeconvolve/
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Analyze specific area of the slide #46

Closed chfloudas closed 6 months ago

chfloudas commented 8 months ago

Hi there, thanks for developing STdeconvolve. Is there a way to define a particular area on the slide and analyze only that, e.g. in case the slide has two sections of tissue or within the same section?

bmill3r commented 8 months ago

Hi @chfloudas,

Thanks for you interest in STdeconvolve! We don't have a function to specifically lasso regions of interest for analysis. However, you can subset the particular spots of interest based on their coordinates in the pos matrix. Then you can use these selected spot indices to select the equivalent rows in the counts matrix.

Hope this helps, Brendan

chfloudas commented 7 months ago

Hi @bmill3r, thanks for the reply! Would the way to do this be found in https://github.com/JEFworks-Lab/STdeconvolve/issues/39?

bmill3r commented 7 months ago

Hi @chfloudas,

That issue is more about rotating the dataset, but using the pos matrix, you can select the locations of interest by filtering on the x and y coordinates.

Brendan

chfloudas commented 7 months ago

Hi @bmill3r , thanks, will try that then!