Stack Overflow
Stack Overflow

Questions tagged [circos]

Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.

79 questions
50
votes
2 answers

Network chord diagram woes in R

I have some data similar to the data.frame d as follows. d <- structure(list(ID = c("KP1009", "GP3040", "KP1757", "GP2243", "KP682", "KP1789", "KP1933", "KP1662", "KP1718", "GP3339", "GP4007", …
Crops
  • 5,024
  • 5
  • 38
  • 65
14
votes
3 answers

'circos' style plots with matplotlib?

Does anybody know if there's a way to make circos-style plots with matplotlib python package, or any other python library? They don't have to be as nice looking as the example.
dimka
  • 4,301
  • 11
  • 31
  • 36
10
votes
5 answers

Installing GD library for perl on MacOSX 10.6

I have been trying to install GD library for perl to no avail a long while now. I've tried every little thing I could find on the internets but nothing. I am trying to get Circos graphs which require the GD package. When I try to install it through…
AhmetZ
  • 137
  • 1
  • 3
  • 9
6
votes
3 answers

R circlize - plot margins and plotting regions

I'm trying to replicate the graphs of this website https://gjabel.wordpress.com/2014/03/28/circular-migration-flow-plots-in-r/ using the r library "circlize". Unfortunately I have two problems: First of all I got a warning for all plotting regions…
sezonzo
  • 63
  • 1
  • 4
6
votes
2 answers

Hello world example for circos?

Can somebody provide me with a "hello world" example for circos? (www.circos.ca) I know there are tons of tutorials provided with the zipped distribution, yet the way I learn is to take the very minimum config and then build from that - and I could…
seinecle
  • 10,118
  • 14
  • 61
  • 120
5
votes
1 answer

How to change label fontsize on circlize chordDiagram in R

I have the following matrix: > circ_mat N chr Y N LG1 N LG2 N PA N chr X N other chr X 1546 128758 109464 71862 6926164 524087 PA 17415 140985 190831 7156005 145783 953412 chr 2 73977 157666 6588917 151092 137082…
Charlie W
  • 99
  • 6
5
votes
0 answers

How to draw track legend in Circos

This Circos tutorial showed configuring spacing between two chromosomes, so track legend can be placed in the area. (source: circos.ca) Like the the example above, but I can't find any explanation about how to draw text there just like right…
Meow
  • 4,341
  • 1
  • 18
  • 17
5
votes
2 answers

R Circlize "Detect some gaps are too large"

I would like make a similar graph posted here using our data, however, I received this error message “Detect some gaps are too large”. Do you think because some values are very small as compare to others (e.g.; 1 versus 1812)?. I made a few changes…
Anthony
  • 67
  • 1
  • 6
4
votes
1 answer

Circlize migration plot missing links

I have tried to follow the R code from Guy, to create circular migration plots. My files are similar to those that he presents with the package "migest" (science/regions_custom). My data file example is 'regions_oceanos': - - - 1 2 4 3 -…
Natalia Bayona
  • 41
  • 2
4
votes
1 answer

Enabling PNG support while installing GD.pm in Perl

I have already installed GD.pm. I want to make sure it supports PNG. So to check that I do this: $ perl -e 'use GD; $im=GD::Image->new(); print $im->can("png") ? "yes" : "no" , "\n";' no As you see. It prints no. Then I download the latest GD from…
pdubois
  • 7,640
  • 21
  • 70
  • 99
4
votes
0 answers

D3 chord diagram with exact positions

I want to create chord diagram in D3, but to specify relations of intervals with exact positions as in the following example by Circos: . Is there a way to do it in D3? If not, is there a way to do it in any other javscript data visualization…
Nikolay Vyahhi
  • 1,432
  • 1
  • 16
  • 30
3
votes
1 answer

Circlize circular barplot as in ggplot

I am trying to duplicate a circular barplot made with ggplot2 into ciclize as follows: While I can bring it into a scatterplot and add a regression: The visualization as barplot interests me more. However I have not found any similar example in…
LuisCol8
  • 69
  • 10
3
votes
1 answer

R: Changing colors on chord diagram in R

Basic question. I have an input table like this: 1 2 3 4 5 6 7 1 0 0 1098 11 137 105 338 2 0 0 351 0 1 0 0 3 0 0 0 132 215 91 191 4 0 0 0 0 6 10 19 5 0 0 0 0 0 37 95 6 0 0 …
Slowat_Kela
  • 1,377
  • 2
  • 22
  • 60
3
votes
2 answers

Adjust highlight.sector() width and placement - Chord diagram (circlize package) in R

I need some help with adjusting highlighted sectors of a chordDiagram() from the circlize package. I am working with fisheries landings data. Fishing vessels start their trip in one port (homeport PORT_DE), and land their catch in another port…
Andronikos K.
  • 105
  • 2
  • 9
3
votes
3 answers

R: circlize circos plot - how to plot unconnected areas between sectors with minimal overlap

I have a data frame with common features between 4 groups of patients and cell types. I have a lot of different features, but the shared ones (present in more than 1 group) are just a few. I want to make a circos plot that reflects the few…
DaniCee
  • 2,397
  • 6
  • 36
  • 59
1
2 3 4 5 6