RCircos.Gene.Connector.Plot: Draw Connectors between Chromosome Ideogram and Gene Names

Description Usage Arguments Author(s) Examples

View source: R/RCircosPlotDataTracks.R

Description

Draw a set of connectors (three lines for each connector) between chromosome ideogram or a data track and gene names. RCircos core components and graphics device must be initialized before drawing.

Usage

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RCircos.Gene.Connector.Plot(genomic.data=NULL, track.num=NULL, 
        side="in", inside.pos=NULL, outside.pos=NULL, 
        genomic.columns=3, is.sorted=FALSE)

Arguments

genomic.data

A data frame with the first four columns for chromosome names, start positions, end positions, and gene names.

track.num

Non-negative integer, representing the ordinal number of the plot track where the connectors are plotted.

side

Character vector, either "in" or "out" representing the position related to chromosome ideogram.

inside.pos

Non-negative numeric, inside position (relative to the centre of plot area) of the track .

outside.pos

Non-negative numeric, outside position (relative to the centre of plot area) of the track.

genomic.columns

Non-negative integer, total number of columns for genomic position in each row. Must be either 3 or 2.

is.sorted

Logic, whether the data is sorted by chromosome names and start positions.

Author(s)

Henry Zhang

Examples

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## Not run: 
library(RCircos)
data(RCircos.Gene.Label.Data)
data(UCSC.HG19.Human.CytoBandIdeogram)

cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;
RCircos.Set.Core.Components(cyto.info, chr.exclude=NULL,  
       tracks.inside=10, tracks.outside=0)

gene.data <- RCircos.Gene.Label.Data
RCircos.Set.Plot.Area()
RCircos.Chromosome.Ideogram.Plot()
RCircos.Gene.Connector.Plot(gene.data, track.num=1, side="in")
RCircos.Gene.Connector.Plot(gene.data, side="out",  
    inside.pos=2.5, outside.pos=3)

## End(Not run)

Example output

RCircos.Core.Components initialized.
Type ?RCircos.Reset.Plot.Parameters to see how to modify the core components.


Not all labels will be plotted.
Type RCircos.Get.Gene.Name.Plot.Parameters()
to see the number of labels for each chromosome.
Not all labels will be plotted.
Type RCircos.Get.Gene.Name.Plot.Parameters()
to see the number of labels for each chromosome.

RCircos documentation built on May 2, 2019, 5:51 a.m.