locus_ggplot: Locus plot using ggplot2

View source: R/locus_ggplot.R

locus_ggplotR Documentation

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",
  xticks = "top",
  xlab = NULL,
  highlight = NULL,
  highlight_col = "red",
  blanks = "fill",
  ...
)

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.

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.

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.

Value

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

See Also

gg_scatter() gg_genetracks()

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")
locus_ggplot(loc)
}

myles-lewis/locuszoomr documentation built on Oct. 25, 2024, 7:24 p.m.