cit.pangenomPlot: cit.pangenomPlot

In FunGeST/Palimpsest: Package

cit.pangenomPlot

Description

pangenomic plot

Usage

cit.pangenomPlot(
  d = NULL,
  ycol = NULL,
  chrom = "chrom",
  pos = "meanPos",
  startPos = "start",
  endPos = "end",
  colorscol = NULL,
  cyto = NULL,
  absPos = "absPos",
  rectangleOption = FALSE,
  plotCentro = TRUE,
  plotCentro.color = "lightgrey",
  plotChrom = TRUE,
  plotnew = TRUE,
  plotyaxis = TRUE,
  plotxaxis = TRUE,
  yaxmark = NULL,
  yaxlab = NULL,
  chromToPlot = c(1:22, "X", "Y"),
  xlim = NULL,
  CexAxis = 0.8,
  ...
)

Arguments

d	data.frame which columns include genomic position information and the wanted y axis
ycol	the column in d to be used as y axis
chrom	the column in d giving the chromosome position
pos	the column in d giving the base pair position (optional)
startPos	the column in d giving the start base pair position
endPos	the column in d giving the end base pair position
colorscol	(optional) column in d giving the color for each point from ycol or a unique color name or number (default black)
cyto	cytoband object (optional)
absPos	the column in d giving the absolute base pair position (will be calculated if not present in d)
rectangleOption	boolean : if TRUE rectangles are plotted instead of points (default) - NB : for points, several 'looks' can be obtained (ex using parameter type , pch,...)
plotCentro	boolean : should centromeric delimitation be plotted ?
plotCentro.color	color of the centromeric delimitation
plotChrom	boolean : should chromosome delimitation be plotted ?
plotnew	boolean : should the a new graph be plotted (default=TRUE), or should something be added to the current graph (->plotnew=FALSE)
plotyaxis	boolean : should an Y axis be plotted ? (considered only if plotnew = TRUE)
yaxmark	y axis 'at' parameter (considered only if plotyaxis = TRUE)
yaxlab	y axis 'labels' parameter (considered only if plotyaxis = TRUE)
chromToPlot	a vector of the chromosomes to be plotted (default c(1:22,"X","Y"))

FunGeST/Palimpsest documentation built on June 2, 2024, 4:21 a.m.