locuszoomr (version 0.3.7)

genetracks: 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",
  italics = FALSE,
  xticks = TRUE,
  xlab = NULL,
  highlight = NULL,
  highlight_col = "red",
  blanks = c("fill", "hide"),
  showRecomb = TRUE,
  align = TRUE
)

Value

No return value.

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.

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.

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.

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')
}