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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.

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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
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'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
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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
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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
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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
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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
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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
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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
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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
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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.
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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
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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
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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
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error installing libgd in mac 10.9

I'm trying to install libgd on my mac OSX 10.9 following the instructions here (https://mikewest.org/2007/04/installing-libgd-from-source-on-os-x) and peaking on some more info here (Installing GD library for perl on MacOSX 10.6). the main goal is…
TriRook
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How to resolve Circos SVG placing text incorrectly?

I have the following Circos diagram, which I rendered as an SVG file and then converted to PNG, for the purposes of illustration: The text labels that circle the outer rim are oriented correctly from 12 o'clock to 9 o'clock, oriented outwards, away…
Alex Reynolds
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