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Add GC content function for plot. #151
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yzhong005
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…b = b-a for link grouping; fixes #29
various smaller fixes and improvements
…ort paths as gggenomes() arguments
improve smart-read backend with new mapping of defined formats, extensions, context and parsers
make genes the first arguement of gggenomes for more intuitive usage. gggenomes() also reads files now
Made it possible to focus on several regions from the same parent sequence at once
Added locate - like focus, but add loci as track instead of zoom; added position_* examples
This is necessary from roxygen 7.3, see https://www.tidyverse.org/blog/2024/01/roxygen2-7-3-0/ and details in https://roxygen2.r-lib.org/articles/namespace.html#s3
quotes are for package names only
Instances found using checkhelper::find_missing_tags() Automatic formatting applied
This version has just been accepted by CRAN 🎉 https://cran.r-project.org/web/packages/gggenomes/index.html
Co-authored-by: x <[email protected]>
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add a function to manually generate the GC content data.frame, which can easily add into the plot.
require(Biostrings)
gc_content<-function (x, seq_id, window)
{#x must be a DNAstrings, can take with readDNAstring, cannot be a DNAstringset
start<-seq(0,(length(x)-window),window)
pick<-function(start){
a<-x[start:(start+window)]
return(a)
}
set<-lapply(start,pick)
gc_test<-rowSums(letterFrequency(DNAStringSet(set), c("G", "C")))/window
gc_test<-data.frame(seq_id=seq_id,start=start,end=start+window,score=gc_test)
return(gc_test)}
an example
seq<-readDNAstring("AA.fasta")
gc<-gc_content(seq, seq_id="a",50)
gggenomes(genes,seqs=seqs,links = links,feats=gc)+
geom_seq()+
geom_gene()+
geom_link(offset = 0.1)+
geom_wiggle(aes(z=score))