gg_genetracks: Plot gene tracks

In myles-lewis/locuszoomr: Gene Locus Plot with Gene Annotations

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",
  xticks = TRUE,
  xlab = NULL,
  highlight = NULL,
  highlight_col = "red",
  blanks = c("fill", "hide")
)

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.
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.

Value

A ggplot2 object.

See Also

locus_ggplot() genetracks_grob()

Examples

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)
}

myles-lewis/locuszoomr documentation built on April 16, 2024, 11:13 p.m.