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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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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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Use circos function in circos

Can someone help me ? How can I add my circos function in my data? when i try i get an error message and it doesn't produce any results I want to do a donut figure like the representation number 1 but i have one other resultat that we can see in the…
Stage
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Software recommendation for circos plot with discrete axis

I would like to make a circos-like plot to visualize SNPs only (with multiple tracks for SNPs attributes). It could be done either with python, R or I am happy to consider other languages. So far, I have taken a look at the circlize R…
Agathe
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R: Group intersections in circos plots showing extra band with variable values

I have a data frame that looks like the following: set.seed(1) mydf <- data.frame() for (g in LETTERS[1:4]){ m <- data.frame(Group=g, Gene=paste(sample(letters[1:4],25,replace=TRUE), sample(1:25,25,replace=FALSE), sep=''), …
DaniCee
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Plot size depending on label size, circlize R package

How can I automatically increase the generated picture when increasing the label size with the cex parameter? With the attached code the labels are not shown completly. install.packages("circlize") library(circlize) pdf("margin_test.pdf") par(mar =…
easelpeasel
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circlize package: tracks with different number of sectors

I'm trying to make a circular diagram using the 'circlize' package in R. I want to make a plot with three tracks, outer track with 36 sectors, middle track with 12 sectors, and inner track with 3 sectors. The sectors in each track should be of equal…
Matt Jago
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In directional Circos plot with circlize, how to widen the end of ribbon?

I am trying to widen the end of ribbon. Is it possible? library(circlize) mat2 = matrix(sample(100, 35), nrow = 5) rownames(mat2) = letters[1:5] colnames(mat2) = letters[1:7] chordDiagram(mat2, grid.col = 1:7, directional = 1, row.col =…
hierophant
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How to make stacked circos plot?

I need to make a circos plot (preferably using circlize or other R package) that should look similar to this one: https://journals.plos.org/plosone/article/figure/image?size=large&id=10.1371/journal.pone.0075072.g003, but I want it to be divided in…
Mieszko
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How to shade custom blocks in Circlize package in R

I am using the R package circlize to create a circos plot. I am aiming to create something similar to Figure 2 in this paper: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004812. I would like to custom specify where to…
Will Hamilton
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Make a matrix out of a df in R

So I have a table that looks something like this name <- c("AGTC","ATTC","ATGC", "ATCC") Var1 <- c("TRA11","TRA8","TRA9", "TRA9") Var2 <- c("TRB1", "TRB15", "TRB7", "TRB7") df <-data.frame(name, Var1, Var2) df name Var1 Var2 1 AGTC TRA11 …
Ahmed Hassan
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R package circlize: circos heatmap colors not showing up

I am trying to create a circular plot using circlize package. When using hex color codes, my plot does not show up anything but when I use actual color names, it shows. Why is that? Code: suppressPackageStartupMessages({ library(tidyverse) …
Komal Rathi
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Circos execution fails due to missing module GD which causes dyld[14230]: missing symbol called

First of all I would like to mention that I am not a programmer and neither do I have an english mother tongue, but I will try to do my best :-) I was looking for a way to create some nice circular visualizations (chord graphs) and stumped across…
deekee
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Problems installing GD for Circos on Mac OS

I am trying to get Circos to install on my Mac (OS Catalina Version 10.15.7) and am having problems with the infamous GD working in perl. I have tried several solutions online and have deleted everything to start from scratch but still cannot get…
Ashley Schumann
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missing GD while installing circos on Mac OS Big Sur Version 11.0.1

I found it is very very hard to install circos on MacOS, and all the answers I can find on Google is pretty rusty and do not work for me on Mac OS Big Sur Version 11.0.1. Here are what I am missing: (base) user@user-MacBook-Pro % circos -modules ok …
Miao Cai
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