locus_plotly: Locus plotly

In myles-lewis/locuszoomr: Gene Locus Plot with Gene Annotations

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,
  gene_col = ifelse(showExons, "blue4", "skyblue"),
  exon_col = "blue4",
  exon_border = "blue4",
  showExons = TRUE,
  maxrows = 8,
  width = 600,
  xlab = NULL,
  blanks = "show",
  ...
)

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.
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.

Value

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

See Also

locus() genetrack_ly() scatter_plotly()

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_plotly(loc)
}

myles-lewis/locuszoomr documentation built on Nov. 29, 2024, 4:49 p.m.