plot ideogram with data

plot ideogram with data for multiple chromosomes

ideogramPlot(
  ideo,
  dataList,
  layout = NULL,
  horiz = TRUE,
  parameterList = list(vp = plotViewport(margins = c(0.1, 4.1, 0.3, 0.1)), ideoHeight =
    unit(1/(1 + length(dataList)), "npc"), vgap = unit(0.3, "lines"), ylabs = "auto",
    ylabsRot = ifelse(horiz, 0, 90), ylabsPos = unit(2.5, "lines"), xaxis = FALSE, yaxis
    = FALSE, xlab = "", types = "barplot", heights = NULL, dataColumn = "score", gps =
    gpar(col = "black", fill = "gray")),
  colorSheme = gieStain(),
  gp = gpar(fill = NA, lwd = 2),
  ...
)

Arguments

ideo

output of loadIdeogram.

dataList

a GRangesList of data to plot.

layout

The layout of chromosomes. Could be a list with chromosome names as its elements.

horiz

a logical value. If FALSE, the ideograms are drawn vertically to the left. If TRUE, the ideograms are drawn horizontally at the bottom.

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.

colorSheme

A character vector of giemsa stain colors.

gp

parameters used for grid.roundrect.

...

parameters not used.

Examples

if (FALSE) { # \dontrun{
ideo <- loadIdeogram("hg38")
library(rtracklayer)
library(grid)
dataList <- ideo
dataList$score <- as.numeric(dataList$gieStain)
dataList <- dataList[dataList$gieStain!="gneg"]
dataList <- GRangesList(dataList)
grid.newpage()
ideogramPlot(ideo, dataList, 
             layout=list("chr1", "chr2", c("chr3", "chr22"), 
                         c("chr4", "chr21"), c("chr5", "chr20"), 
                         c("chr6", "chr19"), c("chr7", "chr18"),
                         c("chr8", "chr17"), c("chr9", "chr16"),
                         c("chr10", "chr15"), c("chr11", "chr14"),
                         c("chr12", "chr13"), c("chrX", "chrY")),
             parameterList = list(types="heatmap", colorKeyTitle="sample1"))
} # }