Bioinformatics Asked on August 21, 2021
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
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()
Correct answer by Ryan SY Kwan on August 21, 2021
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
Answered by Priya on August 21, 2021
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