kplot: Interactive plot of conditioned LOD scores

In simecek/intermediate: eQTl/pQTL Mediation analysis

Description

Plot LOD statistics calculated by mediation.scan against genomic positions. Display a gene name when hovering a mouse over.

Usage

kplot(med, symbol.col = "symbol", chrlen = mouse.chrlen, ...)

Arguments

med	A mediation object
symbol.col	A column of med with gene names
chrlen	A vector with chromosome lengths (as in org.Mm.egCHRLENGTHS)

Value

Htmlwidget iplot

See Also

plot.mediation, mediation.scan

Examples

data(Tmem68)
med <- mediation.scan(target = Tmem68$target,
                      mediator = Tmem68$mediator,
                      annotation = Tmem68$annotation,
                      covar = Tmem68$covar,
                      qtl.geno = Tmem68$qtl.geno)

theme_set(theme_bw())
kplot(med, symbol.col="symbol")

# save the plot as HTML page
gp <- kplot(med, symbol.col="symbol") 
pl <- ggplotly(gp, tooltip="text")
pl
tmpdir <- tempdir()
htmlwidgets::saveWidget(pl, paste0(tmpdir, "/Tmem68.html"),
                        selfcontained=TRUE)
                        

simecek/intermediate documentation built on May 29, 2019, 10:01 p.m.