ggblast: Simple visualization of local blast search output

Description Usage Arguments Examples

View source: R/ggblast.R

Description

The result of blast output using rsko::rblast is dataframe, or local blast output dat with outfmt '6'. The data has these columns, at least, "qseqid", "sseqid", "pident", "qstart", "qend", "sstart", "send", "qlen", "slen","sstrand".

Usage

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ggblast(blast_out, drawtype)

Arguments

blast_out

dataframe: result of rskoseq::rblast output

drawtype

character number: 1: facet_wrap with query id, 2: A panel per query, 3: All in one panel

Examples

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## Not run: 
## sample fasta of Biostrings package
fp <- system.file("extdata", "AtMlos.fna", package="rskodat")
bndb <- "~/db/cdna/TAIR10_cdna" # set you environment
bnout <- rskoseq::rblast(fp, "-", "blastn", bndb, "-num_threads 4")
res1 <- ggblast(bnout, 1)
res2 <- ggblast(bnout, 2)
res3 <- ggblast(bnout, 3)

## End(Not run)

shkonishi/rskoseq documentation built on April 18, 2021, 3:50 p.m.