plot_overrep_kmer: Create a box plot of the log2(observed/expected) ratio across the length of the sequence as well as top
overrepresented kmers. Only ratios greater than 2 are included in the box plot. Default is 20 bins across the length of the sequence and the top 2 overrepresented kmers, but this can be changed by the user.
Description
Create a box plot of the log2(observed/expected) ratio across the length of the sequence as well as top overrepresented kmers. Only ratios greater than 2 are included in the box plot. Default is 20 bins across the length of the sequence and the top 2 overrepresented kmers, but this can be changed by the user.
Usage
plot_overrep_kmer(overkm, bins = 20, top_num = 2, output_file = NA)
Arguments
| Argument | Description |
|---|---|
overkm |
data frame with columns pos, obsexp_ratio, and kmer |
bins |
number of intervals across the length of the sequence |
top_num |
number of most overrepresented kmers to plot |
output_file |
File to write plot to. Will not write to file if NA. Default NA. |
Value
A box plot of the log2(observed/expected ratio) across the length of the sequence
Examples
r
infile <- system.file("extdata", "test.fq.gz",
package = "qckitfastq")
over_km <- overrep_kmer(infile,k=4)
plot_overrep_kmer(over_km)