MakeGeneSchematic: Creates a schematic displaying gene locations in a given...
In jbelsky/TyphoonPlot: Creating Genomic Typhoon Plots

Description Usage Arguments Value Examples

View source: R/create_typhoon_plot_functions.R

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. Currently this function will only make a gene schematic for yeast genes in the sacCer2/SGD R61 genome version.

1
2
3

MakeGeneSchematic(feature_chr, feature_start, feature_end, cex_title = 1,
  bg_type = "white", fwd_gene_col = "gray", rev_gene_col = "gray",
  proteinCoding = T, geneName = T, omit_genes = NA)

`feature_chr`	Character, chromosome (e.g. "1")
`feature_start`	Numeric, genomic start position
`feature_end`	Numeric, genomic end position
`cex_title`	Numeric, specifies the cex expansion factor for the title
`bg_type`	Character, whether to make the background "white" or "transparent" (Default: "white").
`fwd_gene_col, rev_gene_col`	Character, specifies the color for both the Watson (+) and Crick (-) genes (Default: "gray" for both).
`proteinCoding`	Boolean, should only protein-coding genes be included as opposed to including all open-reading-frames (Default: T)
`geneName`	Boolean, should the gene name be displayed (Default: T)
`omit_genes`	Character vector, should any gene names be excluded from the plot. This is useful if there are overlapping genes. (Default: NA)