cpprofile: Carbapenamase Gene Profile

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

Carbapenamase Gene Profile

Description

cpprofile() creates a heatmap of carbapenamase gene profile from the input genome assemblies

Usage

cpprofile(
  outputType = "png",
  width = 2000,
  height = 2000,
  res = 250,
  xlab = "Carbapenamase Genes",
  ylab = "Assembly",
  title = "Carbapenamase Gene Profile Heatmap",
  titlesize = 15,
  labelsize = 12,
  colorcode_low = "#143D59",
  colorcode_high = "#F4B41A",
  cpgcov = 100,
  cpgpident = 100
)

Arguments

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)
xlab	Label on x-axis (default="Carbapenamase Genes")
ylab	Label on y-axis (default="Assembly")
title	Title of the plot (default="Carbapenamase Gene Profile Heatmap")
titlesize	Title size (default=15)
labelsize	Label size (default=12)
colorcode_low	Hex color code for low values (default="#143D59")
colorcode_high	Hex color code for high values (default="#F4B41A")
cpgcov	CP gene coverage cutoff (default=100)
cpgpident	CP gene percentage identity with genomic sequence (default=100)

Examples

cpprofile()
cpprofile(outputType="png", width = 2000, height = 2000, res = 250, xlab="Carbapenamase Genes", ylab="Assembly", title="Carbapenamase Gene Profile Heatmap", titlesize=15, labelsize=12,colorcode_low = "#143D59", colorcode_high = "#F4B41A", cpgcov=100, cpgpident=100)

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