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

Description Usage Arguments See Also Examples

View source: R/methods-grid.R

Description

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

Usage

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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

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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"))

Bioconductor-mirror/MinimumDistance documentation built on July 1, 2017, 5:19 a.m.