isovision: IsoVision

In jsicherman/IsoVision2: Create Isoform Plots

Description

IsoVision

Usage

isovision(
  data,
  whichIsoforms = NULL,
  main = NULL,
  main.cex = 2,
  use.barplot = T,
  barplot.width = 0.1,
  barplot.fill = "white",
  barplot.border = "black",
  line.color = "black",
  intron.reduction = 0.9,
  n.chunks = 1000,
  orf.lwd = 1.5,
  orf.lty = 1,
  norf.lwd = 1,
  norf.lty = 4,
  mar = 0.1,
  terminal.style = "triangle",
  terminal.fill = "white",
  terminal.border = "black",
  default.fill = "white",
  default.border = "black",
  legend.values = setNames(colnames(data)[-(1:8)], colnames(data)[-(1:8)]),
  legend.colors = "Set3",
  filename = "Rplots.pdf",
  width = 11,
  height = 8.5
)

Arguments

data	Data generated by isoviz_data.
whichIsoforms	A character vector of isoform names or an integer vector for isoform ranks to visualize. If null, plots all isoforms.
main	The title.
main.cex	The cex graphical parameter for the title.
use.barplot	Whether or not to plot a barplot of total reads next to the track.
barplot.width	The relative width of the barplot (0.0 to 1.0).
barplot.fill	A vector of colors for the bars. Passed to the R barplot function.
barplot.border	A vector of colors for the border of the bars. Passed to the R barplot function.
line.color	The color of the track lines as a vector of the same length of the number of isoforms, an RColorBrewer palette or a single value.
intron.reduction	The reduction factor for intron widths to ensure long introns are shrunk for plotting.
n.chunks	The number of chunks to split the line into for intron scaling. Higher numbers mean more intron reduction.
orf.lwd	The border weight for exons in the ORF.
orf.lty	The border line type for exons in the ORF.
norf.lwd	The border weight for exons not in the ORF.
norf.lty	The border line type for exons not in the ORF.
mar	The margin.
terminal.style	The drawing style for the terminal exons. Options include "arrow" and "triangle". Any other value will draw a normal rectangular exon.
terminal.fill	The fill color of the terminal exons.
terminal.border	The border color of the terminal exons.
default.fill	The fill color of exons without any annotations.
default.border	The border color of exons without any annotations.
legend.values	A named character with names set to domain annotation names present in data and values set to the preferred "pretty print" name that will show in the legend.
legend.colors	Colors to be applied to domain annotations. Will be applied sequentially in the order that domains are defined in legend.values. Colors will be recycled if length is less than the number of domains in legend.values. Can also be an RColorBrewer palette.
filename	The name to save this plot as.
width	The width, in inches.
height	The height, in inches.

jsicherman/IsoVision2 documentation built on June 10, 2020, 12:35 a.m.