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

Description

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

Usage

pedigreeGrid(g, vps, figs)

Arguments

See Also

plotDenovo pedigreeViewports

Examples

library(VanillaICE)
require(grid)
##marker-level summaries
data(md_exp)
seqlevels(md_exp, force=TRUE) <- "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"))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(MinimumDistance)
Loading required package: VanillaICE
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: GenomicRanges
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to VanillaICE version 1.34.0
Welcome to MinimumDistance version  1.16.0

Attaching package: 'MinimumDistance'

The following object is masked from 'package:VanillaICE':

    acf2

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MinimumDistance/pedigreeGrid.Rd_%03d_medium.png", width=480, height=480)
> ### Name: pedigreeGrid
> ### Title: Plot the log R ratios and BAFs on a grid given by precomputed
> ###   viewports
> ### Aliases: pedigreeGrid
> 
> ### ** Examples
> 
> library(VanillaICE)
> require(grid)
Loading required package: grid
> ##marker-level summaries
> data(md_exp)
> seqlevels(md_exp, force=TRUE) <- "chr22"
> ## segmentation results
> data(md_gr)
> posteriorCalls <- MAP2(md_exp, md_gr, MinDistParam())
> g <- denovoHemizygous(posteriorCalls)
> g
MDRanges object with 3 ranges and 9 metadata columns:
      seqnames               ranges strand |      sample  seg.mean    log_RR
         <Rle>            <IRanges>  <Rle> | <character> <numeric> <numeric>
  [1]    chr22 [17281004, 17633332]      * | md_22169_01   -0.3175   117.288
  [2]    chr22 [17670969, 18670691]      * | md_22169_01   -0.3538   566.107
  [3]    chr22 [19066315, 19792353]      * | md_22169_01   -0.3335   343.433
       log_odds  prob_MAP  prob_222  prob_221       calls number_probes
      <numeric> <numeric> <numeric> <numeric> <character>     <integer>
  [1]       Inf         1         0         1         221            88
  [2]       Inf         1         0         1         221           278
  [3]       Inf         1         0         1         221           208
  -------
  seqinfo: 1 sequence from hg18 genome
> 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"))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>