rview {scruff} | R Documentation |
Visualize read alignments for UMI tagged single cell RNA-sequencing data. Read names must contain UMI sequences at the end delimited by ":". Arrow represents orientation of alignment. Reads are colored by their UMI and sorted by their start positions and UMI.
rview( bamGA, chr = "1", start = 1, end = max(BiocGenerics::end(bamGA)), legend = FALSE )
bamGA |
A GenomicAlignment object |
chr |
Chromosome. Integer or "X", "Y", "MT". |
start |
Genomic coordinate of the start position. |
end |
Genomic coordinate of the end position. |
legend |
Show legend. Default is FALSE. |
A ggplot object of aligned reads
data(bamExample, package = "scruff") g <- rview(bamExample, chr = "MT", legend = TRUE) g