PlotGene: Helper function to plot individual genes as rectangles.

In jbelsky/TyphoonPlot: Creating Genomic Typhoon Plots

Description

Helper function for MakeGeneSchematic to plot individual genes. Each gene is designated as a gray box, with genes on the Watson (+) strand displayed in the top row and genes on the Crick (-) strand displayed on the bottom row. Orientation of the gene name also denotes transcription direction.

Usage

PlotGene(gene.v, y_low, y_high, x_start, x_end, cex_title, geneName,
  x_pos_title = 50, fwd_gene_color, rev_gene_color)

Arguments

gene.v	Vector, selected row from yeast_gene.df feature file containing information about the gene.
y_low	Numeric, the bottom y rectangular coordinate.
y_high	Numeric, the top y rectangular coordinate.
x_start	Numeric, the left x rectangular coordinate of the plot.
x_end	Numeric, the right x rectangular coordinate of the plot.
cex_title	Numeric, specifies the cex expansion factor for the title
geneName	Boolean, should the gene name be displayed (Default: T)
x_pos_title	Numeric, the number of inset bp specifying the gene name.

Value

Rectangle schematic depicting gene coordinates

Examples

 PlotGene(gene.v = yeast_gene.df[1,], y_low = 0.5, y_high = 1,
          x_start = 40000, x_end = 41000, cex_title = 1,
          geneName = T, x_pos_title = 50,
          fwd_gene_color = "gray", rev_gene_color = "gray"
         )

jbelsky/TyphoonPlot documentation built on May 18, 2019, 5:59 p.m.