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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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circlize::circos.heatmap Add gaps between cells

I am creating a circular heatmap as follows: suppressPackageStartupMessages({ library(circlize) }) # input data dput(annot) structure(list(Specimen_Type = c("Both", "Plasma", "Both", "Both", "Plasma", "Plasma", "Plasma", "Both", "Both",…
Komal Rathi
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How to add text to circos graph from data frame in R

I have a df that looks like this X Y A 3 B 6 C 4 D 9 I would like to plot this in a circos graph using circlize with 4 sections. Each section should have the X axis as the title and within the section it should have the Y axis…
user15470345
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Using circlize::draw.sectors inside a function

I would like to make a RGB color scheme using the circlize package. First, I try to make a function so that I only have to input the color and sectors, and the function will do the job Here is the code: colorpallete <- function(color, x){ …
amedicalenthusiast
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Aligning labels in a chordDiagram from circlize package

I have quite a complex circos plot and am having some trouble aligning the labels. To demonstrate the issue I have included a short reproducible example below. I can not figure out how to nicely align every label so that they all sit exactly the…
lmsimp
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Why does this xlim error occur in circlize initialization?

I want to initialize a new chord diagram with circlize, but I'm getting an error that doesn't seem to make any sense given the data I'm feeding into it: Error: Since `xlim` is a matrix, it should have same number of rows as the length of the level…
Andrew Gerlach
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Errors adding genomic feature track in circlize

I'm trying to generate a circos plot with a simple genomic notation from BED files. However, when I use circos.genomeRect this results in an error, or in a track that does not plot rectangles, but semicircles as I show below. Consider the following…
elcortegano
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How to colour labels in R chordDiagram

Following on from this example a few years ago I would like to colour code the segment labels in a chordDiagram using the circlize package in R. Documentation in ?circos.text tells me that I should use the set this using the argument col in the…
lmsimp
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Big and small gaps using circlize in R

How do I group categories so that they appear with big gaps in a chord diagram generated using the circlize package in R? For example, given the following adjacency matrix: A B C D E F G H A 0 0 0 0 0 0 1168 0 B 0 0 2545 278 0…
Lars Rönnbäck
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Expanding the height of sector in 'circlize' and other final touches

Everyone - I'm having some trouble increasing the height of the inside vector of my circlize plot. I'd like it to be large enough to encompass the enlarged labels (see figure). I've been working mainly off this post. I also have a question as to why…
Matt
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How to save R base graphics as an object?

I have a chord diagram built using the circlize package. Unfortunately, it seems like there is no way to save this as an object. I would like to have the plot be an object (especially a ggplot obkect) so that I can modify some of the surrounding…
ldan
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Circular heatmap with R "circlize": Plot area and row labels

I'm trying to plot a single circular clustered heatmap with dendrogram with R "circlize" package. The two column expression data is available from this pastebin link I'm using the following code for plotting, mostly lifted from the circlize…
The August
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Repetitively executing a function in R when my input values are in a DataFrame?

Working in R myData is a DataFrame with 4 columns and B rows X is a number from 1 to B F is a function of D, E, F, and G where D is myData[row X, col 1] E is myData[row X, col 2] F is myData[row X, col 3] and G is myData[row X, col…
Sasha
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Circos plots from unstructured data in R

I have more than 100 observation points (spot), where I looked at particular item (e.g, A, B,C..etc). The basic format of data as follows:…
NoviceStat
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Chord Diagram with transparent links

I have a 8x8 adjacency matrix which looks as follows: I need to visualize only some links within my Chord Diagram, keeping all the 8 sectors. I tried to reproduce the instructions provided here: R Circlize, Chord graph with empty sectors So I…
Connectome
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How to create adjacency matrix for gene-gene interactions from RNA-Seq (circlize input)

I'm profiling tumor microenvironment and I want to show interactions between subpopulations that I found. I have a list of receptors and ligands for example, and I want to show that population A expresses ligand 1 and population C expresses receptor…
lozzib
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