So I'm performing an ATAC-seq analysis using ArchR software and have had the same error persisting when running the following:
p <- ggPoint( # ggPoint: a ggplot-based dot plot wrapper function x = df[,1], y = df[,2], colorDensity = TRUE, continuousSet = "sambaNight", xlabel = "Log10UniqueFragments", ylabel = "TSS Enrichment", xlim = c(log10(500), quantile(df[,1], probs = 0.99)), ylim = c(0, quantile(df[,2], probs = 0.99)) ) + geom_hline(yintercept = 4, lty = "dashed") + geom_vline(xintercept = 3, lty = "dashed")
Error in df[, 1]: object of type 'closure' is not subsettable
I have also tried switching out the brackets for parantheses but this does not fix the error. Any suggestions?