pedigreeGrid {MinimumDistance} | R Documentation |
Plot the log R ratios and BAFs on a grid given by precomputed viewports
pedigreeGrid(g, vps, figs)
g |
a |
vps |
a list of viewports. See |
figs |
a list of trellis objects created by the function |
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"))