pedigreeGrid: Plot the log R ratios and BAFs on a grid given by precomputed...

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

Description

Plot the log R ratios and BAFs on a grid given by precomputed viewports

Usage

pedigreeGrid(g, vps, figs)

Arguments

g	a MDRanges object
vps	a list of viewports. See pedigreeViewports.
figs	a list of trellis objects created by the function plotDenovo.

See Also

plotDenovo pedigreeViewports

Examples

library(VanillaICE)
require(grid)
##marker-level summaries
data(md_exp)
seqlevels(md_exp, pruning.mode="coarse") <- "chr22"
## segmentation results
data(md_gr)
posteriorCalls <- MAP2(md_exp, md_gr, MinDistParam())
g <- denovoHemizygous(posteriorCalls)
g
vps <- MinimumDistance:::pedigreeViewports()
param <- HmmTrellisParam()
p <- plotDenovo(md_exp, g[1], param)
p <- pedigreeGrid(g=g[1], vps=vps, figs=p)
leg <- mdLegend(g[1])
upViewport(0)
pushViewport(vps[["legend"]])
grid.text(leg, x=unit(0.02, "npc"), y=unit(0.95, "npc"), just=c("left", "top"),
          gp=gpar(cex=0.6, fontfamily="mono"))
##
## combine adjacent denovo hemizygous
##
g2 <- reduce(denovoHemizygous(posteriorCalls), min.gapwidth=500e3)
post <- MAP2(md_exp, g2)
g2 <- denovoHemizygous(post)
p <- plotDenovo(md_exp, g2, param)
p <- pedigreeGrid(g=g2, vps=vps, figs=p)
leg <- mdLegend(g2)
upViewport(0)
pushViewport(vps[["legend"]])
grid.text(leg, x=unit(0.02, "npc"), y=unit(0.95, "npc"), just=c("left", "top"),
          gp=gpar(cex=0.6, fontfamily="mono"))

rscharpf/MinimumDistance documentation built on Sept. 16, 2019, 4:12 a.m.