Circos is a software package for visualizing data and information. It visualizes data in a circular layout — this makes Circos ideal for exploring relationships between objects or positions.
Questions tagged [circos]
79 questions
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Circos plot in python
I'm trying to plot a circos diagram using pycircos
Code:
import pandas as pd
import pycircos
import matplotlib.pyplot as plt
Garc = pycircos.Garc
Gcircle = pycircos.Gcircle
d = {
'A': ['study1', 'study2', 'study3'],
'B': ['study1',…
Natasha
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1 answer
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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1 answer
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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0 answers
How to set/add overall chart padding to Circos/Chord in d3 graph?
How to add chart overll padding for circos/chord chart?
I have similar kind of chord chart with same attributes please see given link [https://www.d3-graph-gallery.com/graph/chord_basic.html].
Actually I want to set overall chart…
0
votes
1 answer
layout_circle using ggbio pulling data from a .csv
I'm trying to pullout the data of my chromosome size which is stored on a .csv. Went I try to graph that information I get the next error: "Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function 'layout_circle'…
Ale
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3 answers
Best approach to visualise presence/absence of events in multiple groups
I have a dataset where the presence/absence of mutations in 40 particular genes has been recorded comparing normal tissue (e.g. lung tissue) vs a tumour from that tissue (e.g. lung tumor) for twenty tissue types. I am struggling to find the best way…
user964689
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1 answer
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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1 answer
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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- 3
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1 answer
GraphViz dot Circular Node Alignment
How to use Graphviz to align nodes circular in clusters with additional text? Optionally with identical node positions (always 8 nodes per cluster)?
I tried circo, however, faced some shortcomings:
No clustering
No comments
Problems with margins…
braggPeaks
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1 answer
R: Sorting Sectors in Chord Diagram based on Width?
I'm using Chord Diagrams in R (via the Circlize/Circos packages) to visual name associations in a dataset. I was able to generate the Chord Diagram (as shown below):
However, I don't know how to sort each sector (or each name) based on its…
superasiantomtom95
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1 answer
Error: attribute d: Expected number, "….43564672524005LNaN,NaNZ"
I tried to get running circosJS but I got the following errors with my data:
1 "datum" "unknown parent id" {line: 1, value: undefined, header: "sourceId", layoutSummary: {…}}
circos.js:19573 1 "datum" "unknown parent id" {line: 2, value: undefined,…
user977828
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I got an empty web site with circosJS
I have the following chords.js file
var gieStainColor = {
gpos100: 'rgb(0,0,0)',
gpos: 'rgb(0,0,0)',
gpos75: 'rgb(130,130,130)',
gpos66: 'rgb(160,160,160)',
gpos50: 'rgb(200,200,200)',
gpos33: 'rgb(210,210,210)',
gpos25:…
user977828
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1 answer
Using CircosJS how to link layout's divs
I'm kind of new to d3js and I'm trying to use this one module : https://github.com/nicgirault/circosJS
I've made a plunker on what I'm stuck : https://plnkr.co/edit/8Sn0quYr5teCv239W9k6?p=preview
How can I link months between them ?
Here's is my JS…
RVA
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1 answer
Trouble in installing Font::TTF module
I failed to install the module through cpan Font::TTF.
I'm on strawberry perl 5.24, windows 8 32bit.
C:\Users\user>cpan
Loading internal null logger. Install Log::Log4perl for logging messages
There seems to be running another CPAN process (pid…
Jiang Bo
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1 answer
Installing Circos: Problems installing GD module on Mac OS
I would like to install Circos. I followed the instructions on Circos website. In particular, I checked for missing perl modules. I'm missing several of them:
missing Font::TTF::Font
missing GD
missing …
Antonin
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