MakeGenPlot: Make Genomic Plots Function

In uashogeschoolutrecht/scPlot: Plot

Description

Make Genomic Plots Function

Usage

MakeGenPlot(g_url = NULL, f_url = NULL, dl_folder = NULL,
  chr_id = NULL, gen_name = NULL, start = 1, end = 10000,
  show_gene_id = FALSE)

Arguments

g_url	Url to the ".gtf" file of the researched genome on the ncbi website. when the url is the same as the .fna file (exept for the ".fna"), only the fnaUrl is enough.
f_url	Url to the ".fna" file of the researched genome on the ncbi website.
dl_folder	Path to the folder to download the files in.
chr_id	Chromosome ID name of the researched chromosome, as named in the gff and gtf files. As character. Default is the first chromosome.
gen_name	Name to store the downloaded files, and title name of the plot. The name of the organism without spaces is recommended. As character.
start	Base start of plot.
end	Base end of plot.
show_gene_id	Show the gene ID instead of the product in the plot. Logical. The gene ID is needed to get the sequence of a gene in function GetSequenceNow.
gene_only	Show only the Gene or also start and stop codons? Logical.

Value

A plot of the inserted genome files.

Examples

MakeGenPlot(g_url = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/277/835/GCF_002277835.1_ASM227783v1/GCF_002277835.1_ASM227783v1_genomic.gtf.gz",
           dl_folder = "C:/Users/Downloads",
           chr_id = "NZ_NQOT01000381.1",
           gen_name = "Flavobacterium_ir1",
           start = 80000,
           end = 90000,
           show_gene_id = FALSE,
           f_url = NULL)

uashogeschoolutrecht/scPlot documentation built on Nov. 23, 2019, 11:27 a.m.