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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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Show different data in top and bottom of Rcirclize

I have 2 dataframes with different number of rows and columns, and I'd like to show both of them in a circos plot with circlize. My data looks like…
Sos
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Unable to go beyond karyotype command in circos using perl command line application

I am working on Circos with a objective to create a circos plot. This is my very first attempt. I do not have any coding background. Currently I am trying to use .txt file already available with the installation, karyotype.human.txt. I am using…
Hemalatha Athawale
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Circos heatmap how to split by labels?

I can't split with circle heatmap with external labels but not spliting circos.heatmap library(circlize) colores1 = colorRamp2(c(0,0.5,1,2,3,4), c("lightblue1","Orchid1","Orchid4","maroon2","maroon4",…
Israel Muñoz Velasco
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Responsive sizing on dashbio Circos / D3 Chord Diagram

Hey so I'm using dashbio circos which is chord diagram library built on D3's chord diagram. The circos (chord diagram) has a property called size, which you write a number to to set the size of the chord diagram. (If you don't set a size, then it…
danknyc
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R package - Transferring environment from imported package

Assume an R package (myPackage) that imports the R package RCircos via the DESCRIPTION file and the NAMESPACE file. $ cat DESCRIPTION Package: myPackage Imports: RCircos (>= 1.2.0) ... $ cat NAMESPACE import(RCircos) ... One of the perks of…
Michael Gruenstaeudl
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Plotting genomic data using RCircos package

I am trying to use the RCircos package in R to visualize links between genomic positions. I am unfamiliar with this package and have been using the package documentation available from the CRAN repository from 2016. I have attempted to format my…
Jenny
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Simple, non-ribbon chord diagram (Python 2.7)

I am looking to replicate a plot similar to this: with the following criteria: NON-ribbon connections between points (thin lines) Text outside each dot Only 10 or so points, instead of the 30+ shown above. Additional colors (lines/text) not…
AaronJPung
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Circlize plot - Does not draw clear lines

I have this script, which results in this really pretty circlize plot. install.packages('circlize', repos = "http://cran.rstudio.com/" ) install.packages('data.table', repos =…
Meeldurb
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How to reduce edge length between specific nodes in circo engine graphviz

enter image description hereHow can I reduce the edge length of specific nodes in circo engine of graphviz. Here is the simple dot file of 19 nodes and 22 edges. I compiled using the command: circo "input-filename" -Gstart=5 -Gsize=1,2! -Gdpi=300…
ksn
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How to create an interval file defined by values from another file - for circos imaging of WGS data

I am trying to depict my whole-genome sequence (WGS) data of my parasite, using the circos software. One of the elements I would like to depict, is the areas of the reference genome for which i do not have sequencing data from my parasite. I order…
Sidsel
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Control colors of links based on source and target nodes in edgebundleR

This question can be considered to be an extension of Network chord diagram woes in R Is it possible to change the colors of the links in the plot based on whether the node on which the cursor is set is a source node or a target node as done in the…
Priyanka Basu
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R (circlize): How to remove self links?

Here is an example code: df <- rbind(matrix(rep(sample(5),2),5,2),matrix(sample(10),5,2)) model_color <- unique(as.vector(df)) names(model_color) <- model_color brand <- unique(as.vector(df)) names(brand) <- brand chordDiagram(data.frame(df),…
dcirillo
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Graphviz compacting graph

I'm generating a graph with graphviz and the circo tool it provides. The graph generated is a nice shape, but the lengths of the edges between the nodes are a lot larger than they need to be, which makes the text of the nodes be small (relative to…
Danack
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Cleanest way to modify a circos image

I would like some advice on the following: I've created an image with circos (dna data). I want to annotate this data by plotting a gene name in the middle of the plot, and an arrow to show where the first gene starts. (an example output file here:…
MrFronk
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R Circlize, Chord graph with empty sectors

I am trying to create a chord graph using the circlize package in R. I would like to include sectors for which there is no outflow (no links emanating from them). Is there a way to: Force the program to report rows from my data frame, even if there…
george
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