Hi, thanks for developing Signac!
When I run CoveragePlot() with the same parameters, I do not get the same plot each time. I thought max.downsample and downsample.rate was what causes the random sampling of positions, but even when I set the downsample.rate to 1 (which to my understanding means to retain all of the positions) the plots do not come out to be the same each time I run the function. I also tried to change the smoothing window size, but cannot control the outcome of the smoothing function. Could you suggest if there is a parameter I can specify to make the same plot with the same parameter values, while reflecting a reliable number of counts at each peak?
Plots I obtained from the two times I ran the same codes:
Codes used to produce the above 2 plots:CoveragePlot( object = nmglut, region = "GRIN2A", features = "GRIN2A", annotation = T, expression.assay = "SCT", region.highlight = StringToGRanges(c("chr16-9735961-9737093", "chr16-9787990-9788950", "chr16-10079470-10081122")), assay.scale = "common", group.by = "timextype.ident", ymax = 700, downsample.rate = 1, extend.upstream = 100000, extend.downstream = 100000 )
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