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Questions tagged [circlize]

circlize is a free, open-source, R language implementation of the circos software for visualizing data in a circular format.

The circlize package is an implementation of the circos data visualization software. Originally designed for visualizing genomics data, these graphics are ideal for exploring complex relationships between objects or positions.

For examples of circlize R package, visit http://jokergoo.github.io/circlize.

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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 reflect 3 relationships in a Chord Diagram and avoid label overlap?

I am trying to great a chord diagram that reflects a 3 way connection that goes from the individual sample to species to what label it falls under. However when I try to create my chord diagram some of my labels are overlapping and you cant see what…
IzOss
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Circular heat maps in R?

Similar questions have been asked here and here, however, none of the other answers solve my problem. Im trying to join together two (or more) separate heat maps and turn them into a circle. Im trying to achieve something like the image below (which…
Electrino
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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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Adding extra track to outside of circos plot (circlize, chordDiagram)

I'm trying to recreate this figure below, where the "to" variable (i.e. target genes) is further grouped into outer (labelled) categories (i.e. receptors). I have generated some example data, unfortunately I'm not sure what format is needed for the…
Gordon Beattie
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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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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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chordDiagram with highlighted, undirected and limited edges (R)

I would like to display a network of certain projects (A01,...,Q04) and their collaborations (edges). It should be possible to highlight all the edges from one projects to the others (in yellow). This is the current result. I have three problems, I…
lukascbossert
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circos.heatmap(): Error in rowMeans(m) : 'x' must be an array of at least two dimensions

I'm following the tutorial to make circular plots in R. Suppose I have this dataset: set.seed(123) mat1 = rbind(cbind(matrix(rnorm(50*5, mean = 1), nr = 50), matrix(rnorm(50*5, mean = -1), nr = 50)), …
amedicalenthusiast
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Add percentage labels inside bars in circos.barplot in Circlize

I was able to create a stacked bar chart like this: library(circlize) library(vegan) # for `reorder.hclust` (may be masked by the library `seriation`) library(dendextend) # for `color_branches` t=read.table(text="Kalmyk 0.119357 0.725057 0.000010…
nisetama
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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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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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How to Save Circlize Chord Diagram as a graphic object

I created a chord diagram in R using the circlize package. I noticed that this graphic is not being saved as a ggplot object. I am trying to make the graphic an object so I can export it to excel. Any suggestions?…
ldan
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Different version of GlobalOptions package in R

I'm trying to install the package "circlize" and I am having trouble resolving what seems to be a simple error. When I run: install.packages("circlize") It says: Installing package into ‘*file location*/3.2’ (as ‘lib’ is unspecified) Warning in…
N22V
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R: Sort links by distance to sectors in chord diagramm with circlize

is it possible to sort the links in each sector of a chord diagram made with the circlize package by distance to the other sectors? Normally, links could overlap near the tracks because of their position. This would be prohibited by changing it…
danceb
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