locus_ggplot: Locus plot using ggplot2

Description

Genomic locus plot similar to locuszoom.

Usage

locus_ggplot(
  loc,
  heights = c(3, 2),
  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 = 12,
  text_pos = "top",
  italics = FALSE,
  xticks = "top",
  xlab = NULL,
  highlight = NULL,
  highlight_col = "red",
  blanks = "fill",
  ...
)

Value

Returns a ggplot2 plot containing a scatter plot with genetracks underneath.

Arguments

loc: Object of class 'locus' to use for plot. See locus().
heights: Vector supplying the ratio of top to bottom plot.
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.
...: Additional arguments passed to gg_scatter() to control the scatter plot, e.g. pcutoff, scheme, recomb_offset etc.

Details

Arguments to control plotting of the gene tracks are passed onto gg_genetracks() and for the scatter plot are passed via ... to gg_scatter(). 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 = 'IRF5', flank = c(7e4, 2e5), LD = "r2",
             ens_db = "EnsDb.Hsapiens.v75")
locus_ggplot(loc)
}