locus_plotly: Locus plotly

Description

Genomic locus plot similar to locuszoom, using plotly.

Usage

locus_plotly(
  loc,
  heights = c(0.6, 0.4),
  filter_gene_name = NULL,
  filter_gene_biotype = NULL,
  cex.text = 0.7,
  italics = FALSE,
  gene_col = ifelse(showExons, "blue4", "skyblue"),
  exon_col = "blue4",
  exon_border = "blue4",
  showExons = TRUE,
  maxrows = 8,
  width = 600,
  xlab = NULL,
  blanks = "show",
  ...
)

Value

A 'plotly' plotting object showing a scatter plot above gene tracks.

Arguments

loc: Object of class 'locus' to use for plot. See locus().
heights: Vector controlling relative height of each panel on 0-1 scale. Alternatively a vector of length 2 of height in pixels passed to scatter_plotly() and genetrack_ly().
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)
cex.text: Font size for gene text.
italics: Logical whether gene text is in italics.
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.
width: Width of plotly plot in pixels which is purely used to prevent overlapping text for gene names.
xlab: Title for x axis. Defaults to chromosome seqname specified in locus.
blanks: Controls handling of genes with blank names: "fill" replaces blank gene symbols with ensembl gene ids. "hide" completely hides genes which are missing gene symbols. "show" shows gene lines but no label (hovertext is still available).
...: Optional arguments passed to scatter_plotly() to control the scatter plot.

Details

This is an R/plotly version of locuszoom for exploring regional Manhattan plots of gene loci. Use locus() first to generate an object of class 'locus' for plotting. This references a selected Ensembl database for annotating genes and exons. Hover over the points or gene tracks to reveal more information.

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_plotly(loc)
}