xyplotList {VanillaICE} | R Documentation |
Data for the graphic is generated by a call to grangesData
.
xyplotList(granges, se, param = HmmTrellisParam()) ## S4 method for signature 'HmmGRanges,SnpArrayExperiment' xyplotList(granges, se, param = HmmTrellisParam()) ## S4 method for signature 'GRangesList,SnpArrayExperiment' xyplotList(granges, se, param = HmmTrellisParam()) xygrid(trellis_plot, viewports, granges)
granges |
a |
se |
a |
param |
trellis parameters for plotting HMM |
trellis_plot |
an object of class |
viewports |
a list of viewports as provided by the |
if(require("BSgenome.Hsapiens.UCSC.hg18")){ bsgenome <- BSgenome.Hsapiens.UCSC.hg18 snp_exp <- getExampleSnpExperiment(bsgenome) seqlevels(snp_exp, pruning.mode="coarse") <- "chr22" fit <- hmm2(snp_exp) g <- reduce(hemizygous(fit), min.gapwidth=500e3) trellis_param <- HmmTrellisParam() fig <- xyplotList(g, snp_exp, trellis_param) vps <- viewports() xygrid(fig[[1]], vps, g) }