plotOnIdeo: Plot data superimposed on chromosomal ideogram

In shraddhapai/IdeoViz: Plots data (continuous/discrete) along chromosomal ideogram

Description

Plot data superimposed on chromosomal ideogram

Usage

plotOnIdeo(chrom = stop("enter chromosome(s) to plot"), ideoTable, 
    values_GR, value_cols = "values", plotType = "lines", 
	 col = "orange", 
    bpLim = NULL, val_range = NULL, addScale = TRUE, scaleChrom = TRUE, 
    vertical = FALSE, addOnetoStart = TRUE, smoothVals = FALSE, 
	cex.axis = 1,plot_title = NULL, ablines_y = NULL, cex.main=1, ...)

Arguments

chrom	(character) chromosome(s) to create ideograms for
ideoTable	(data.frame) ideogram table. See getIdeo()
values_GR	(GenomicRanges) data to be plotted must be in metadata columns
value_cols	(character) which series to plot. Should be column names of the mcols() slot of values_GR
plotType	(character) Plot type for each series. Values can be "lines" or "rect" to plot lines or barplots respectively. The latter is not recommended when several series are to be plotted on the same axis.)
col	(character) vector of colors for data series. If provided as a named vector, will use the metadata column "group" to code points by colour. This option is available for plotType="seg_tracks" only.
bpLim	(numeric) (xlim); display only a section of the chromosome and the corresponding values
val_range	(numeric) (ylim); y-axis scale for data series
addScale	(logical) if TRUE, bp positions will be shown along the chromosomes. This feature should be turned off if numerous chromosomes' worth of data are being plotted and all objects don't fit on the final graphics device.
scaleChrom	(logical) if FALSE, all chroms will display as the same size. scaleChrom will be ignored if bpLim is not NULL
vertical	(logical) if TRUE, chromosomes will be plotted vertically
addOnetoStart	(logical) if TRUE, adds 1 to chromStart. Useful to convert data in half-open coordinates - which is all data from the UCSC genome browser, including cytoBandIdeo, into 1-base.
smoothVals	(logical) if T, smoothes each trendline. Currently hard-coded to lowess smoothing with span=0.03
cex.axis	(integer) axis font size
plot_title	(character) title for overall graph
ablines_y	(numeric) when supplied, draws reference lines on the y-axis
cex.main	(numeric) font size for plot title.
...	other graphing options for barplot (i.e. main="Values", to title bar plot "Values")

Details

Main function to plot binned data alongside chromosomal ideogram. plotOnIdeo() is the main function of this package. It is the one the end-user is expected to call to generate plots. Input is provided as a GRanges object (values_GR), with data to be plotted contained in its metadata slot. The user is responsible for providing pre-binned data, if binning is required. Data can also be binned using the avgByBin() function in this package. The ideogram table (ideoTable) is the same as the cytoBandIdeo table available from the UCSC genome browser database for a given genome is a can be either automatically downloaded from UCSC (see getIdeo()) or read in from a local-file and passed to this function.

There are numerous arguments which control the appearance of the plot. The main decision points are:

1. vertical: Whether the entire plot should have a horizontal or vertical orientation

2. plotType: One of [rect|lines|seg_tracks]. Type of plot, trendline ("lines"), barplot ("rect") or tracks of GenomicRanges (seg_tracks). "rect" only works when there is a single data series (single set of values) to be plotted on the same axis.

Other considerations:

• The size of the graphics device limits the number of chromosomes that can be plotted. A simple solution may be to set addScale=FALSE. However, it is recommended to call plotOnIdeo() multiple times, and plotting a fewer number of chromosomes on each page.

• The code expects coordinates of values_GR to be in 1-base. Set addOneToStart=TRUE if supplied coordinates are in 0-base.

Examples

data(binned_multiSeries)
data(hg18_ideo)
plotOnIdeo(chrom=seqlevels(binned_multiSeries),
ideoTable=hg18_ideo, values_GR=binned_multiSeries, 
value_cols=colnames(mcols(binned_multiSeries)), col=1:5)

shraddhapai/IdeoViz documentation built on April 27, 2020, 10:36 p.m.