gg_genetracks: Plot gene tracks

Description

Plot gene annotation tracks from ensembldb data using ggplot2 and grid.

Usage

gg_genetracks(
  loc,
  filter_gene_name = NULL,
  filter_gene_biotype = NULL,
  border = FALSE,
  cex.axis = 1,
  cex.lab = 1,
  cex.text = 0.7,
  gene_col = ifelse(showExons, "blue4", "skyblue"),
  exon_col = "blue4",
  exon_border = "blue4",
  showExons = TRUE,
  maxrows = NULL,
  text_pos = "top",
  italics = FALSE,
  xticks = TRUE,
  xlab = NULL,
  highlight = NULL,
  highlight_col = "red",
  blanks = c("fill", "hide")
)

Value

A ggplot2 object.

Arguments

loc: Object of class 'locus' generated by locus().
filter_gene_name: Vector of gene names to display.
filter_gene_biotype: Vector of gene biotypes to be filtered. Use ensembldb::listGenebiotypes() to display possible biotypes. For example, ensembldb::listGenebiotypes(EnsDb.Hsapiens.v75)
border: Logical whether a bounding box is plotted.
cex.axis: Specifies font size for axis numbering.
cex.lab: Specifies font size for axis titles.
cex.text: Font size for gene text.
gene_col: Colour for gene lines.
exon_col: Fill colour for exons.
exon_border: Border line colour outlining exons (or genes if showExons is FALSE). Set to NA for no border.
showExons: Logical whether to show exons or simply show whole gene as a rectangle. If showExons = FALSE colours are specified by exon_border for rectangle border and gene_col for the fill colour.
maxrows: Specifies maximum number of rows to display in gene annotation panel.
text_pos: Character value of either 'top' or 'left' specifying placement of gene name labels.
italics: Logical whether gene text is in italics.
xticks: Logical whether x axis ticks and numbers are plotted.
xlab: Title for x axis. Defaults to chromosome seqname specified in locus.
highlight: Vector of genes to highlight.
highlight_col: Single colour or vector of colours for highlighted genes.
blanks: Controls handling of genes with blank names: "fill" replaces blank gene symbols with ensembl gene ids. "hide" hides genes which are missing gene symbols.

Details

This function is called by locus_ggplot(), and in turn it calls genetracks_grob(). It can be used to plot the gene annotation tracks on their own as a ggplot2 object.

gene_col, exon_col and exon_border set colours for all genes, while highlight and highlight_col can optionally be used together to highlight specific genes of interest. For full control over every single gene, users can add columns gene_col, exon_col and exon_border to the TX object within the 'locus' object. Columns added to TX override their equivalent arguments.

Examples

Run this code

if(require(EnsDb.Hsapiens.v75)) {
data(SLE_gwas_sub)
loc <- locus(SLE_gwas_sub, gene = 'IRF5', flank = c(7e4, 2e5), LD = "r2",
             ens_db = "EnsDb.Hsapiens.v75")
gg_genetracks(loc)
}