PlotGene: Helper function to plot individual genes as rectangles.

Description Usage Arguments Value Examples

View source: R/create_typhoon_plot_functions.R

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

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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

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 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 June 5, 2017, 5:12 p.m.