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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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Is there a way to alphabetize groups within a circular visualization in R using circos.heatmap?

I use R and "circlize" package. I'm trying to create a circular heatmap and I want to sort them alphabetically within the groups. However, I couldn't find how to do it. How can I achieve this? To produce this graph the code is…
mereda
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When using R package circlize to draw a PDF image , there will be redundant lines, why? How to eliminate redundant lines

I used the R package circlize to draw a PDF image (Figure 1)fig.1. The display of images viewed through R studio zoom and WPS(a type of PDF reader) is shown in Figure 1. However, when I opened the PDF through AI, a large number of redundant lines…
user22055406
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Cell padding in circlize circos.genomicDensity()

I want to add a track to a circos plot using the circlize package in R to visualize gene density across a genome. When using the circos.genomicsDensity() function, however, it looks like the gene density line does not spread through the total…
Anthony Piot
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How can I choose the track to place custom labels in a chord diagram?

I want to add a set of custom labels outside the most external track on a chord diagram, however, the labels appear in the interior of the diagram and I can't figure out how to specify their location. Here's a reprex with the basic structure of my…
Lumimoto
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R Package Circlize for heatmaps, how to split my data?

I need to make a heatmap for RNA expression in different types of cancer. I would like to do it with circlize, and divide my circle in 5 parts (each part is one type of cancer). I couldn't figure out how to input the data and make the circle divided…
Kathleen Yasmin Almeida
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Graphics devices do not work in for loop in R

I am working on a single nucleus RNA sequencing dataset with samples from two different conditions and 4 timepoints each. I would like to run the same analysis on all of those timepoints for 4 different celltypes and wrote a for loop that seems to…
Smeerlap
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Circlize in R: Reducing gaps between sectors (gap.after) and adjusting the default ticks marks

Using the package circlize from R, My objective is to be able to reduce the default gaps generated between the sectors in the chord diagram. According to the manual, this is possible by passing the gap.after command within the circos.par command.…
Purrsia
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How can I solve this error to visualize the gene fusion using the circlize package?

I want to visualize several gene fusions in a circle using the circlize package in R. My data is fusion1 <- data.frame("chr" = c("chr7", "chr1", "chr12", "chr3", "chr16", "chr7", "chr12", "chr1"), "start" = c(27934839, 92327028,…
Ji Seon Jeong
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r circlize: missing value where TRUE/FALSE needed

I am trying to plot (for the first time) a chord diagram in the package circlize in R Studio. I am going through the manual chapters (Circular Visualization in R). The first step is to allocate the sectors on a circle by using the circos.initialize…
Purrsia
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Log scale circlize barplot

Is it possible to add a log scale to a circlize barplot axis? I would like add a y-axis with a scale of 0.1, 1, 10, 100 to a circular barplot created using the package circlize. I have not been successful yet finding a way using circos.yaxis. Is it…
Gary_fri
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R circlize: Inputing data and barplot

I am trying to input this dataframe into a circular format using the package "circlize" dataframe: Value Location 1 22.64237 Front 2 12.53842 Left 3 70.00000 Center 4 39.83154 Right 5 13.22489 Rear I'd like each "Value" to be visualised…
Gary_fri
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"invalid value specified for graphical parameter "omi"" while trying to use gridOMI() in R

I am trying to create a Chord diagram in R using the circlize package by following the examples from https://jokergoo.github.io/circlize_book/book/legends.html. This works fine, but I run into errors trying to insert some figure legends using the…
Jari van Diermen
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Fix axis numbering in Circlize chord diagram and font issues

I have been experimenting with the 'circlize' package but I have been having issues with my axis label spacing. I wanted to customize the axis labelling to have major ticks at a specified intervals. I succeeded using the below code, but my issues…
Dustin
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Constrain axis limits in chordDiagram (circlize) when making gifs

I hope somebody will be able to help me with this chordDiagram visualisation I am trying to create. I am well aware that maybe this visualization type was not suitable for this particular data, but somehow it was something I had in my head (or how I…
kardemummabulle
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chordDiagram: color gradients for links between groups

My question is about the function 'chordDiagram' of the 'circlize' package in R. I wonder if there is a possibility to color the links between the different groups with a smooth color gradient of the two groups. We set the colors of the groups with…
Nicolas Leclercq
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