Entering edit mode
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.
- Primer.Name Gene start end sample Percent_reads_mapped
- primer_221_LEFT 5prime_UTR 27 51 SMP000122632 0.008607884
- 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.
Here are some tools that might give you and idea: https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag=Coverage
Thank you so much. This is great.