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.

Usage

genetracks(
  locus,
  filter_gene_name = NULL,
  filter_gene_biotype = NULL,
  border = FALSE,
  cex.axis = 0.9,
  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"),
  showRecomb = TRUE,
  align = TRUE
)

Arguments

locus	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.
showRecomb	Logical controls alignment of right margin if recombination data present.
align	Logical whether to set par() to align the plot.

Details

This function is called by locus_plot(). It can be used to plot the gene annotation tracks on their own. It uses base graphics, so layout() can be used to position adjacent plots above or below.

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

No return value.

Examples

if(require(EnsDb.Hsapiens.v75)) {
data(SLE_gwas_sub)
loc <- locus(SLE_gwas_sub, gene = 'UBE2L3', flank = 1e5,
             ens_db = "EnsDb.Hsapiens.v75")
genetracks(loc)

## Limit the number of tracks
genetracks(loc, maxrows = 4)

## Filter by gene biotype
genetracks(loc, filter_gene_biotype = 'protein_coding')

## Customise colours
genetracks(loc, gene_col = 'grey', exon_col = 'orange',
           exon_border = 'darkgrey')
}

myles-lewis/locuszoomr documentation built on Nov. 29, 2024, 4:49 p.m.