Gene coverage plots from a data frame on tiling amplicon sequencing data
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11 weeks ago
pramach1 ▴ 30

I have a data frame that has the percent of reads per sample mapped to every tiling amplicon across the genome.

1. Primer.Name Gene start end sample Percent_reads_mapped
2. primer_221_LEFT 5prime_UTR 27 51 SMP000122632 0.008607884
3. primer_221-2_LEFT 5prime_UTR 31 56 SMP000122632 0.009914841

This is a data frame, without a BAM file and other metadata. If I have to plot a coverage plot using a data frame like this, what would be the best visual to use. To ask the question differently, if I do a line plot, with the gene names on the x axis which is not continuous variable, it doesn't work. Thank you for the help.

I have tried using ggcoverage, that uses geom_coverage.

g <- ggplot() + geom_coverage(data= data, mark.region = mark.region, range.position = "out")


The visual is not something I was expecting.

visualization coverage sequencing plots R • 471 views
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Thank you so much. This is great.