plotChromValuePair: Base function which plots the ideogram and superimposed data...
In IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram

Description Usage Arguments Details See Also Examples

Base function which plots the ideogram and superimposed data for a single chromosome. plotOnIdeo() calls this function and stacks the resulting output.

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plotChromValuePair(chrom, cytoTable, bpLim, vertical, 
values_GR,val_range, col, value_cols = "values", default_margins, 
addScale, ablines_y, smoothVals, span=0.03, verbose = FALSE, ...)

`...`	arguments to `axis()`, `line()`, and `rect()`
`chrom(character)`	chromosome(s) to create ideograms for
`cytoTable(data.frame)`	loaded ideogram table. (see ideoTable argument to plotOnIdeo())
`bpLim(numeric)`	(aka xlim); display only a section of the chromosome and the corresponding values
`vertical(logical)`	if TRUE, chromosomes will be plotted vertically
`values_GR(list`	or GenomicRanges) If plotType is "lines" or "rect", the function expects this to be a GRanges() object with data series in metadata columns. If plotType is "seg_tracks" this is a list of GRanges(), each entry of which represents a track.
`val_range(numeric)`	(aka ylim); y-axis scale for data series
`col(character)`	colour for series
`value_cols(character)`	column name for series to plot
`default_margins(numeric)`	page inner margins (in inches)
`addScale(logical)`	if FALSE, bp positions will be hidden
`ablines_y(numeric)`	when specified, will draw reference lines on the y-axis
`smoothVals(logical)`	when T applies loess() to each series
`span(numeric)`	loess::span()
`verbose(logical)`	print messages

Plots one unit of chromosome ideogram with dataseries superimposed. Usually, the user can avoid this function and directly call plotOnIdeo(). However, this function may be used in cases where further plot customization is required.

plotOnIdeo()

data(hg18_ideo)
data(binned_multiSeries)
layout(matrix(1:2, byrow=TRUE,ncol=1),heights=c(2.5,1))
plotChromValuePair("chr1",hg18_ideo, 
	values_GR=binned_multiSeries,
value_cols=colnames(mcols(binned_multiSeries)),plotType='lines',
	col=1:5,val_range=c(0,10),bpLim=NULL,vertical=FALSE,addScale=TRUE,
ablines_y=NULL,smoothVals=FALSE,default_margins=c(0.5,.5,.1,.1))