upsetR_plot: UpsetR - Set intersection plot visualization

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

UpsetR - Set intersection plot visualization

Description

upsetR_plot() generates set intersection plot of CP genes across all the input genome assemblies.

Usage

upsetR_plot(
  outputType = "png",
  width = 2000,
  height = 2000,
  res = 250,
  xlab = "Carbapenamase Gene Set Size",
  ylab = "Number of genome assemblies",
  cpgcov = 100,
  cpgpident = 100,
  order.by = "degree",
  nsets = 40,
  number.angles = 0,
  point.size = 1.5,
  line.size = 1,
  sets.bar.color = "red"
)

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")
cpgcov	CP gene coverage cutoff (default=100)
cpgpident	CP gene percentage identity with genomic sequence (default=100)
order.by	How the intersections in the matrix should be ordered by (default="degree")
nsets	Number of sets to look at (default=40)
number.angles	The angle of the numbers atop the intersection size bars (default = 0)
point.size	Size of points in matrix plot (default=1.5)
line.size	Width of lines in matrix plot (default = 1)
sets.bar.color	Color of set size bar plot (default= "red")

Examples

upsetR_plot()
upsetR_plot(outputType="png", width = 2000, height = 2000, res = 250, xlab="Carbapenamase Gene Set Size", ylab="Number of genome assemblies",cpgcov=100, cpgpident=100, order.by = "degree",nsets = 40, number.angles = 0,point.size = 1.5, line.size = 1,sets.bar.color = "red")

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