plotOneIdeo {trackViewer}R Documentation

plot ideogram with data for one chromosome

Description

plot ideogram with data for one chromosome

Usage

plotOneIdeo(ideo, dataList, parameterList = list(vp =
  plotViewport(margins = c(0.1, 4.1, 1.1, 0.1)), ideoHeight = unit(1/(1 +
  length(dataList)), "npc"), vgap = unit(1, "lines"), ylabs =
  seqlevels(ideo)[1], ylabsRot = 90, ylabsPos = unit(2.5, "lines"), xaxis =
  FALSE, yaxis = FALSE, xlab = "", types = "barplot", heights = NULL,
  dataColumn = "score", gps = gpar(col = "black", fill = "gray")),
  chrom = seqlevels(ideo)[1], colorSheme = gieStain(), gp = gpar(fill
  = NA, lwd = 2), ...)

Arguments

ideo

output of loadIdeogram.

dataList

a GRangesList of data to plot.

parameterList

a list of parameters for each dataset in the dataList. The elements of the parameters could be xlabs, ylabs, etc. type could be barplot, line, point, heatmap.

chrom

A length 1 character vector of chromosome name.

colorSheme

A character vector of giemsa stain colors.

gp

parameters used for grid.roundrect.

...

parameters not used.

Examples

## Not run: 
ideo <- loadIdeogram("hg38")
library(rtracklayer)
library(grid)
dataList <- ideo[seqnames(ideo) %in% "chr1"]
dataList$score <- as.numeric(dataList$gieStain)
dataList <- dataList[dataList$gieStain!="gneg"]
dataList <- GRangesList(dataList, dataList)
grid.newpage()
plotOneIdeo(ideo, dataList, chrom="chr1")

## End(Not run)



[Package trackViewer version 1.20.2 Index]