visGenome: Visualize Genome Properties

In HajkD/seqstats: A Statistical Analysis Package for Biological Sequences

Description

This function allows to visualize selected properties of input genomes such as:

• gene length distribution: stats_type = "length_distr"

Usage

visGenome(data, seq_type, stats_type = "length_distr", ...)

Arguments

data	a file path to a fasta file storing either DNA, CDS, or protein sequences.
seq_type	sequence type stored in the fasta file specified in data. Available options are: seq_type = "dna": the fasta file specified in data contains a DNA alphabet. seq_type = "cds": the fasta file specified in data contains coding sequences (CDS) (DNA alphabet). seq_type = "protein": the fasta file specified in data contains a protein alphabet.
stats_type	a character string specifying the genome feature that shall be visualized: "length_distr", ... .
...	additional parameters that shall be passed to the corresponding plot function.

Value

a plot object.

Author(s)

Hajk-Georg Drost

Examples

## Not run: 
# download the proteome of Arabidopsis thaliana from refseq
# and store the corresponding proteome file in '_ncbi_downloads/proteomes'
# install.packages("biomartr")
Ath_proteome <- biomartr::getProteome( db = "refseq",
             organism = "Arabidopsis thaliana" )

# visualize the length distribution of the proteome of A. thaliana
visGenome(data = Ath_proteome,
          seq_type = "protein",
          stats_type = "length_distr", 
          main = "Histogram of A. thaliana protein sequence lengths",
          xlab = "Sequence Length",
          breaks = 100)

## End(Not run)

HajkD/seqstats documentation built on April 26, 2020, 8:03 p.m.