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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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Chord diagram for plotting inter-relationships between continuous data points

I would like to plot pairwise inter-relationships between numerical data points in the style of a mixed circular scatterplot and a chord diagram. In contrast to a "real" chord diagram, I only have a single sector with pairs of circular continuous…
atreju
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Circlize plot - Histograms with same Y axis

I'm using the pakage circlize to draw histograms of two different bed (dataframes). I could do the histograms in two diffrerent tracks using the "circos.trackHist" function, but I cant compare them because they have different scales in the Y axis.…
Nicolás Spoto
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How to create a circular multi-histogram graph using the R package circlize?

I apologize in advance since I am a beginner user in R. I have a big data file, with multiple factors (15), and multiple tested samples from various group within each factor (5). I have calculated the means for each group within each factor. To…
adam.bj
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How to zoom a circular dendrogram in R?

I have this circular dendrogram in R and I want to zoom it. How can I proceed? Here it is: The following code was used: library(dendextend) library(circlize) load(file = "hc1.rda") #out1 <- cutree(hc1, k = 50) load(file = "out1.rda") dend <-…
Marilou
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Making a plot in circlize package in R

I have airline connectivity data among different cities. I would like to make a chord diagram with control in color with help of Circize package. I need help…
NoviceStat
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R: circlize chord diagram with images as labels?

Is it possible to place images where the labels of a circlize chordDiagram would be? For example, I have manually placed SVG outlines of the continents against the labels. I was wondering if there is a programmatic way to achieve this. Here is a…
tchakravarty
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Error when plotting chordDiagram in circlize: "Error in circos.initialize"

I am getting a persistent error when I attempt to plot a chordDiagram in circlize (R). I am able to generate the plot fine with one data set (Data1), but not with another (Data2), which is structurally identical (as far as I can tell). Both data…
Alice
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Error 'undefined columns selected' - Chord diagram (circlize package) in R

I need some help with an error message returning when using the chordDiagram() function from the circlize package. I am working with fisheries landings. Fishing vessels start their trip in one port (homeport PORT_DE), and land their catch (scallops…
Andronikos K.
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R circlize chord and grid colouring

I have a dataset with two columns. One is the data category and one is my samples. I am using mtcars as an example library(circlize) library(data.table) mtCARS<- mtcars setDT(mtCARS, keep.rownames = TRUE)[] mtCARS1<-…
Behzad Rowshanravan
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How to transform data from frame/datatable to matrix in R for a Chord Diagram?

This may seem relatively simple, but I'm trying to change data from a data frame into a matrix as I'm working with the new D3 chorddiag package. Before I've used circlize and depended on using the dataframe capabilities. Chorddiag seems to rely…
LoF10
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R circlize chord diagram with log scale

Is it possible to make a chord diagram in the circlize package that displays log10 values? So far I have been able to produce a plot with correct size links, but the corresponding axis will not match up. the axis displays the sum of all links/logged…
Koalaitystats
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R: Adjusting Labels in circlize diagram

I have the code below which im trying to make into a circular diagram using the amazing package circlize I have read the vigenette and admit some of it has gone over my head a bit, I was wondering if there is a quick way to remove all the labels on…
John Smith
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supplying user defined color in r circlize package

I am trying create circle diagram using circlize package in R. Here example where I use random color: require(circlize) circos.par("default.track.height" = 0.1, cell.padding = c(0, 0, 0, 0)) circos.initializeWithIdeogram(plotType = NULL) bed1 =…
SHRram
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