bio_gene_locations: Gene Locations

In KatrionaGoldmann/BioOutputs: Visualisation of Biological Data

Gene Locations

Description

This function produces ggplot and plotly plots showing the genes in a genomic range

Usage

bio_gene_locations(
  chromosome = 6,
  xrange = c(2.8e+07, 3.4e+07),
  subset_genes = c(),
  font_size = 3,
  ggtheme = theme_null(),
  output_plots = TRUE,
  ens_version = "EnsDb.Hsapiens.v75",
  stat = "gene_level",
  label_col = ifelse(stat == "gene_level", "symbol", "tx_id")
)

Arguments

chromosome	Which chromosome are you looking at
xrange	chromosome position
ggtheme	ggplot theme to give plots.
output_plots	Logical whether to output plots
ens_version	The EnsemblDB version. You will need this package installed. Options include: "EnsDb.Hsapiens.v75", "EnsDb.Hsapiens.v86"...
stat	The plotting stat for autoplot (either 'gene_level' for gene level annotation or 'tx_level' for transcript level annotation)
label_col	The column to label genes/transcripts by from the EnsemblDB. Options include those in 'EnsDb.Hsapiens.v75@tables$gene' or ‘EnsDb.Hsapiens.v75@tables$tx' (depending on stat), for example: ’gene_id', 'tx_id', 'symbol', 'entrezid', ...
subset_gene	List of genes to plot/subset to within xrange

Examples

bio_gene_locations()

KatrionaGoldmann/BioOutputs documentation built on May 21, 2022, 1:24 p.m.