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stuart-lab / signac

R toolkit for the analysis of single-cell chromatin data
https://stuartlab.org/signac/
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Transcription factor footprinting #406

Closed l-magnificence closed 3 years ago

l-magnificence commented 3 years ago

When I performed motif footprinting analysis from the signac footprinting vignette in my own dataset, the motif object set in seurat was 0x0 and there occur an error in functon PlotFootprint: Error in (ncol(x = x) - background):ncol(x = x) : argument of length 0. So I created motif assay directly in Motif analysis vignette , and then run footprint and PlotFootprint function, but it still occur an error: Error in (ncol(x = x) - background):ncol(x = x) : argument of length 0.

code: tmp <- Footprint( object = tmp , motif.name = features, genome = BSgenome.Hsapiens.UCSC.hg38 ) image

PlotFootprint(tmp, features = features) image

timoast commented 3 years ago

Please include the full code you're running and the output of sessionInfo()

l-magnificence commented 3 years ago

I found the reason why this error occured. One of the cell types in my data has number 1 ,so it can't extract data in GetFootprintData function. When I deleted this cell, it run greatly.

timoast commented 3 years ago

Ok this should now be fixed on the develop branch. See the website for installation instructions