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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Pass different files as parameters
I have a few queries with regards to Circos plots.
I want to include a legend within the plot to indicate what does the different circles within the plot represent.
I want to rename the plot sub-routines in a way that when I run circos I can use…
Ankur Chaturvedi
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Understanding START and END of LINKS in CIRCOS
I'm reading the tutorials and got problems understanding the start and end of a link.
For example, here are 3 links between hs1 and /hs[2-4]/
ID start end ID start end
hs1 100 200 hs2 250 300
hs1 400 550 hs3 500 750
hs1 600 800 …
kbxu
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get perl GD to work
I am trying to get the GD perl module to work on my mac. I have installed the gd library
$ gdlib-config --all
GD library 2.1.0
includedir: /usr/local/include
cflags: -I/usr/local/include
ldflags: -L/usr/X11/lib -L/usr/local/lib
libs: …
user3266890
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How to get rid of histogram grids in Circos
I am using Circos to plot some histograms. How can I get rid of the vertical grids in the example below?
pasta
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ModuleNotFoundError for pycirclize
For generating circos plots, used the following command to install pycirclize
pip install pycirclize
command ran properly. But when tried executing
from pycirclize import Circos
error thrown.
Error message
ModuleNotFoundError: No module named…
Subrat mohapatra
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1 answer
How to create a circos plot
I've 50 COVID samples (PE fastq reads) along with clades and lineage data for each sample. I am doing a phylogenetic analysis.My workflow to produce the tree is as following:
raw reads (.fastq) --> assembly (SPades) --> RagTag (scaffolding) -->…
Vinit24
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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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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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Reduce distance between nodes in circo layout
I have a graph with circo layout which generates some nodes (highlighted on the screenshot) too far from the root. I would like to reduce the distance between highlighted nodes and the root node in red square.
Graph definition is quite…
user2250152
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How to build a circos plot on differential expression data from microarray and RNA-seq using Python?
I have differential expression data from both microarray and RNA-seq experiments, and I would like to visualize the data using a circos plot in Python. Can anyone provide me with guidance on how to achieve this?
Specifically, I would like to…
Mirrah
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Iterate through list of DFs, grab their listname and apply a function?
I have a list of data frames which are named correctly in the list. I want to create circos plots using those data frames and save them using a for loop.
Here is the script where I create the plot:
jpeg("df-name.jpeg")
circos.initialize(df$sectors,…
mervebduman
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Converting sequence of SVG images (which contain Emojis) to a MPEG video
I googled and even asked chatGPT but I'm unable to find a solution and hope to get some guidance here.
First I've to mention that I'm not a programmer but rather a beginner.
Following a short description of what I'm trying to achive and what I've…
deekee
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Matplotlib plots distorted shapes instead of a polygon and a wedge
I am trying to add a function to the pycircos module written by ponnhide on https://github.com/ponnhide/pyCircos/blob/master/pycircos/pycircos.py. I tried to add a circular arrow in the circular plot, which is a patch collection from a ring and an…
Karim Yosef Rezk
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Make a multilayered circos plot in R from a dataframe
I want to make a circos plot from a data frame consisting name of country (first column), fruit (second column) and category (third column). My rule is that if the row of second and third column matches, the corresponding countries are considered to…
Discovery2020
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Downloading GD with support for png, jpeg, Freetype, and Fontconfig for Circos
I've been trying to download the software Circos on MacOS, and it requires that I download GD with support for PNG, JPEG, Freetype, and FontConfig. I've been following the directions on…
