locus_plot: Locus plot

Description

Genomic locus plot similar to locuszoom.

Usage

locus_plot(
  loc,
  filter_gene_name = NULL,
  filter_gene_biotype = NULL,
  xlab = NULL,
  cex = 1,
  cex.axis = 0.9,
  cex.lab = 1,
  cex.text = 0.7,
  use_layout = TRUE,
  heights = c(3, 2),
  showExons = TRUE,
  maxrows = 7,
  xticks = "bottom",
  border = FALSE,
  gene_col = ifelse(showExons, "blue4", "skyblue"),
  exon_col = "blue4",
  exon_border = "blue4",
  text_pos = "top",
  italics = FALSE,
  highlight = NULL,
  highlight_col = "red",
  blanks = "fill",
  recomb_col = "blue",
  ...
)

Value

No return value.

Arguments

loc: Object of class 'locus' to use for plot. See 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)
xlab: x axis title.
cex: Specifies size for points.
cex.axis: Specifies font size for axis numbering.
cex.lab: Specifies font size for axis titles.
cex.text: Font size for gene text.
use_layout: Logical whether graphics::layout is called. Default TRUE is for a standard single plot. Set to FALSE if a more complex layout with multiple plots is required e.g. using multi_layout().
heights: Ratio of top to bottom plot. See layout.
showExons: Logical whether to show exons or simply show whole gene as a rectangle
maxrows: Specifies maximum number of rows to display in gene annotation panel.
xticks: Character value of either 'top' or 'bottom' specifying whether x axis ticks and numbers are plotted on top or bottom plot window.
border: Logical whether a bounding box is plotted around upper and lower plots.
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.
text_pos: Character value of either 'top' or 'left' specifying placement of gene name labels.
italics: Logical whether gene text is in italics.
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.
recomb_col: Colour for recombination rate line if recombination rate data is present. Set to NA to hide the line. See link_recomb() to add recombination rate data.
...: Other arguments passed to scatter_plot() e.g. index_snp, pcutoff, scheme, recomb_offset, etc, and arguments for plot() e.g. ylab, main, etc to control the scatter plot.

Details

This is an R version of locuszoom for generating publication ready Manhattan plots of gene loci. It references Ensembl databases for annotating genes and exons. Use locus() first to generate an object of class 'locus' for plotting. LDlink web server can be queried using function link_LD() to retrieve linkage disequilibrium (LD) information on the index SNP.

Arguments to control plotting of the gene tracks are passed onto genetracks() and for the scatter plot are passed via ... to scatter_plot(). See the documentation for each of these functions for details.

Examples

Run this code

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

## Use embedded LD information in column `r2`
loc2 <- locus(SLE_gwas_sub, gene = 'IRF5', flank = c(7e4, 2e5), LD = "r2",
              ens_db = "EnsDb.Hsapiens.v75")
## Add label for index SNP
locus_plot(loc2, labels = "index")
}