rdataframebioinformaticsbioconductorgenomicranges
How to calculate length distribution and coverage distribution bed file
I have dataset in bed file and I want to calculate and plot the length and coverage distribution of file. How can I calculate length distribution in R.
df1:
chr21 2800 3270
chr21 3600 4152
chr2 3719 5092
chr22 3893 4547
chr2 339 5092
chr22 3563 3597
structure(list(df1c = c("chr21", "chr21", "chr2", "chr22","chr2"), df1c2 = c(2800,
3600, 3719, 3893,339,3563), df1c3 = c(3270, 4152, 5092, 4547,5092,3597)), class = "data.frame", row.names = c(NA,
-4L))
Solution
You could do:
library(tidyverse)
df %>%
mutate(id = factor(seq(nrow(.)))) %>%
ggplot(aes(y = df1c2, x = df1c, xend = df1c, yend = df1c3)) +
geom_segment(aes(y = 1, yend = max(df1c3)), size = 8, lineend = 'round',
color = 'gray20') +
geom_segment(size = 7, aes(color = 'coverage')) +
coord_flip() +
labs(color = '', y = 'Location', x = 'Chromosome') +
theme_light(base_size = 16)
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