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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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103 questions
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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
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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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Put labels inside the legend color bar in circlize chord diagram

I've been following the circular visualization in R tutorial. I try to recreate the figure in Chapter 16 A complex example of Chord diagram. Particularly, I am asking on how to make the labelled legend for 'Chromatin States', i.e. to label each box…
amedicalenthusiast
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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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Implementing ggvis with shiny and circlize

I'm trying to understand how ggvis works in the context of shiny and it's been a real headache. At this point I'm just trying to make something, anything interactive. Ideally I would like to be able to filter data points with sliders and be able to…
adarvishian
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Set sector width of chord diagram with circlize

I have a data set involving 100 people and their diagnosis of 5 medical conditions. Any combinations of conditions can occur, but I've set it up so that the probability of condition D depends on condition A, and E depends on B.…
emudrak
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Add a title to the graph generated using the R circlize package

How can I added a title to the circos plot generated using the circlize package, please? I didn't find any reference in the manual.
Grace
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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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r circlize report gap.degree is too large

I'm trying to plot chord with chordDiagram function in R.circlize package, the reference code similar to "matrix visualization" set.seed(999) chordDiagram(mat) circos.clear() the error report like: circos.initialize(factors = factors, xlim = xlim)…
telehan
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How to fill incomplete axis lines in chord diagram?

In the migration example dataset with code provided at [https://www.data-to-viz.com/graph/chord.html], why in some objects, axis line does not extends beyond max values. For example, in South East Asia, Europe and West Asia, axis line is not…
gnuser23
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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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Cluster circular heatmap based on categorical variable

I want to plot a circular heatmap similar to the image below (obtained from here). However, I want to cluster by clin.info$subtype column, which correspond with the column names of meth and exp. library(circlize) library(ComplexHeatmap) # Split by…
melolili
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Circlize Error: Since `gap.degree` parameter has length larger than 1, it should have same length as the number of sectors

I want to plot a chord diagram using the circlize library. The gap.degree parameter is defined as the gap between two neighbour sectors. It can be a single value or a vector. If it is a vector, the first value corresponds to the gap after the first…
melolili
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Circlize in R: Multiple group chord diagram

Using the package circlize from R, My objective is to be able to group a chord diagram by year within each sector. New to the package, I started from the beginning by following examples in the tutorial. According to the vignette, grouping is…
Purrsia
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