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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.

Vignettes

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Inconsistent figures with R png() device when type is changed

I've made a chord diagram (from circlize package) for population movement and when I tried saving it using type="cairo-png" from png() device, it gives me a different one to the default png() device or the one seen from R studio plot panel. Below is…
M_Shimal
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find center and add text to the circos plot

The center of the circle (a,b) can be derived from the circle equation
Sathish
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Create nested similarly-named sectors using circlize in R

I'm trying to use the circlize package to create a circos plot in which the outer track has unique sector names (10 names), and within each unique sector, there are 2 categories of file types. The two categories are the same for each of the 10 names…
Zoey RW
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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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Labelling circular dendextend dendrogram

I'm trying to plot a circular dendrogram of compositional data. Using the following code: library(dendextend) library(circlize) library(compositions) data("Hydrochem") hydro<-Hydrochem d <- dist(hydro[7:19], method="euclidean") hc <- hclust(d,…
Scott
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r chord-diagram circlize --> rotating names

I am writing because I would like to get some help with a plot in R, using the package circlize, please. I am trying to make a chord diagram, and I could make it, but the names on the plot are overlapped, then I tried with a code that I picked up…
naxo
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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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Circlize chord diagram with multiple levels of data

I am finding myself a bit stuck, I want to show flows between regions for trafficked species via a chord diagram on circlize, but am unable to work out how to plot when column 1 and 2 represent the "connection", column 3 is the "factor" of interest…
Koalaitystats
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How do you specify seperate sets of y axis limits for each sector of a circlize plot?

I have three sets of data that I want to plot using Circlize. Set's "a" and "b" contain positive and negative values, set "c" contains only positive values. I want to plot using a consistent y axis for "a" and "b" and different one for "c".…
Dominic
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how to increase the radius in circlize plot

I have drawn the following plot using the circlizepackage. The red circle is the unit circle drawn afterwards, using plotrix. I want to plot the first track outside the red unit circle. For this reason I changed canvas.xlim and canvas.ylim to…
Mark Heckmann
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How to use library(circlize) in R when matrix is not symmetric

I am trying to draw a flow map using the circlize library. My code is below and the dataset (i75_from_flow.RData) is here: https://drive.google.com/file/d/0B0hTmthiX5dpbFJFc2hfN1Zqd1k/view library(reshape) t1 <- cast(i75_from_flow, ORIGFIPS ~…
Krishnan
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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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Grouping track in the package circlize in R

I have created a plot similar to the one on page 8 of the circlize tutorial here: http://cran.r-project.org/web/packages/circlize/vignettes/genomic_plot.pdf Now I am trying to overlay an additional track on top of the gene names, which shows…
user971102
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circlize in R to make a circular plot

Im trying to make a circular plot similar to gene expression plots. I found the circlize package in R could do this, and Im trying to follow this http://cran.r-project.org/web/packages/circlize/vignettes/genomic_plot.pdf I manage to get to: 6.…
user2335015
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How to present variations in Likert scale with a circular plot?

I have recorded the answers, in the form of a Likert scale from 0 to 10, of ten subjects regarding a specific believe "before" and "after" a treatment. The answers, as well as the sex assigned at birth, have been stored in a df where column 1…
Lorenzo
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