RCircos.Workflow: A Simple RCircos Plot Workflow

Description Usage Author(s) Examples

View source: R/RCircosMain.R

Description

Print out on screen to list procedures for a basic RCircos plot.

Usage

1

Author(s)

Henry Zhang

Examples

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## Not run: 
library(RCircos)
RCircos.Workflow()

## End(Not run)

Example output

1. Load RCircos library:

   library(RCircos)

2. Load chromosome cytoband data:

   data(UCSC.HG19.Human.CytoBandIdeogram);
   cyto.info <- UCSC.HG19.Human.CytoBandIdeogram;

   # Other chromosome ideogram data installed:
   # UCSC.Mouse.GRCm38.CytoBandIdeogram
   # UCSC.Baylor.3.4.Rat.cytoBandIdeogram

3. Setup RCircos core components:

   RCircos.Set.Core.Components(cyto.info, chr.exclude=NULL,
                    tracks.inside=10, tracks.outside=0);

4. Load input data:

   heatmap.data <- read.table("/path/Heatmap.data.txt", 
                        sep="\t", quote="", head=T);
   hist.data <- read.table("/path/histgram.data.txt", 
                        sep="\t", quote="", head=T);
   link.data <- read.table("/path/link.data.txt", 
                        sep="\t", quote="", head=T);

5. Modify plot parameters if necessary:

   rcircos.params <- RCircos.Get.Plot.Parameters()
   rcircos.params$radiu.len <- 1.5;
   RCircos.Reset.Plot.Parameters(rcircos.params);

6. Open graphic device:

   RCircos.Set.Plot.Area();

   or submit your own code. For example: 

   par(mai=c(0.25, 0.25, 0.25, 0.25));
   plot.new();
   plot.window(c(-2.5,2.5), c(-2.5, 2.5));

7. Call plot function to plot each data track:

   RCircos.Chromosome.Ideogram.Plot();
   RCircos.Heatmap.Plot(heatmap.data, data.col=5, 
                        track.num=1, side="in");
   RCircos.Histogram.Plot(hist.data, data.col=4, 
                        track.num=4, side="in");
   RCircos.Link.Plot(link.data, track.num=5, 
                        by.chromosome=FALSE);

8. Close the graphic device if you was plotting to file:

   dev.off();

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