1
$\begingroup$

I am using Rcircos to make a chromosome ideogram plot for my gene list (n = 45). However, I am getting this error:

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

I am using the below-given script and what to know is there any way to fit all my genes in the chromosome ideogram plot

 library(RCircos)
 data(UCSC.HG19.Human.CytoBandIdeogram)
 RCircos.Set.Core.Components(
 cyto.info=UCSC.HG19.Human.CytoBandIdeogram, 
 chr.exclude = NULL, 
 tracks.inside = 10, tracks.outside = 0) 
 
 #Making a plot with RCircos
 out.file <- "RCircos_IF.pdf";
 pdf(file=out.file, height=8, width=8, compress=TRUE);
 RCircos.Set.Plot.Area();
 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));

 # plot chromosome ideogram
 RCircos.Set.Plot.Area();
 RCircos.Chromosome.Ideogram.Plot() 
 gene.lable.data = read.table ("IF.txt", sep="\t", header=T, row.names = 1) # IF.txt is my input file
 RCircos.Gene.Connector.Plot(gene.lable.data, track.num = 1, side = "in");
 track.num <- 2;
 RCircos.Gene.Name.Plot(gene.lable.data,name.col = 4, track.num)

 dev.off()

My input file looks like

    Chromosome  chromStart  chromEnd    Gene.name
    1   chr1    150363091   150476566   RPRD2
    2   chr1    150549369   150560937   ADAMTSL4
    3   chr1    91949371    92014426    BRDT
    4   chr1    31365625    31376850    FABP3
    5   chr1    150960583   150975004   CERS2
$\endgroup$
2
$\begingroup$

To change the maximum number of genes in RCircos, we could modified the char.width according to this link. The actual value in a RCircos session could be modified with get and reset methods for plot parameters.

params <- RCircos.Get.Plot.Parameters() #$char.width
params$char.width <- 100 #default 500
RCircos.Reset.Plot.Parameters(params)

#the maxLabels are updated accordingly
RCircos.Get.Gene.Name.Plot.Parameters()
$\endgroup$
0
$\begingroup$

Just want to add that apart from params$char.width, we can also use

params$text.size
params$text.size <- 0.2 #default 0.4
params$base.per.unit < 50000 #imp #default value = 30000
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.