assemblystat: Generate assembly statistics from input genomes assemblies...

In ramadatta/CPgeneProfiler: Profiles the Carbapenamase genes from the genome assemblies (One Line, Title Case)

Generate assembly statistics from input genomes assemblies (FASTA)

Description

assemblystat() generates basic assembly stats which includes N50 size, N90 size and Genome assembly size. This function also generates Assembly Size vs N50 plot and Assembly Size vs N50 plot

Usage

assemblystat(
  fastalocation,
  outputType = "png",
  width = 700,
  height = 700,
  res = 150,
  geom_point_size = 3,
  n50colorfill = "#0072B2",
  n90colorfill = "#D55E00"
)

Arguments

fastalocation	Location of the folder with only fasta files. The files must have extensions with either .fasta or .fa format
outputType	Output result file in pdf/tiff/jpeg/png format (default="tiff")
width	width of the device (default=2000)
height	height of the device (default=2000)
res	Nominal resolution in ppi (default=250)
geom_point_size	point size (default=3)
n50colorfill	Hex color code of N50 plot (default= "#0072B2")
n90colorfill	Hex color code of N90 plot (default= "#D55E00")

Examples

assemblystat()
assemblystat("/home/user/CPgeneProfiler/testData/fasta", outputType="png", width = 700, height = 700, res = 150, geom_point_size=3, n50colorfill = "#0072B2", n90colorfill = "#D55E00")

ramadatta/CPgeneProfiler documentation built on Jan. 9, 2025, 4:22 a.m.