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produce a plotly display of statistics of xQTL association

Source: R/viz.R
viz_stats.Rd

produce a plotly display of statistics of xQTL association

Usage

viz_stats(
  se,
  jitter_fac = 500,
  ptcolor = "blue",
  midchop = 2,
  xlabel = "SNP addr",
  ylabel = "xQTL association Z"
)

Arguments

se

SummarizedExperiment post "bind_Zs"

jitter_fac

plot employs jittering of SNP address by this factor

ptcolor

point color

midchop

stats with absolute value less than this value are omitted from display

xlabel

axis label

ylabel

axis label

Examples

data(geuv19xse)
sds = MatrixGenerics::rowSds(assay(geuv19xse), na.rm=TRUE)
qq = quantile(sds, .8)
ok = which(sds > qq)
lk = geuv19xse[ok,]
mafs = maf(lk) 
mins = apply(data.matrix(mcols(getCalls(lk))), 1, min, na.rm=TRUE)
lk = filterCalls(lk, which(mafs>.25 & mins > -1))
lk <- bind_Zs(lk)
#> some variants have MAF > 0.5 
viz_stats(lk)