circlize protocols

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circlize specifications

Information


Unique identifier OMICS_04658
Name circlize
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 0.4.4
Stability Stable
Requirements
methods, stats, grid, graphics, utils, grDevices, knitr, gridBase, colorspace, R(≥3.0.0), png, GlobalOptions(≥0.1.0), shape, dendextend(≥1.0.1), ComplexHeatmap(≥1.13.2)
Maintained Yes

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Documentation


Maintainers


  • person_outline Zuguang Gu <>
  • person_outline Benedikt Brors <>

Publication for circlize

circlize in pipeline

2018
PMCID: 5882890
PMID: 29615742
DOI: 10.1038/s41598-018-23860-y

[…] factor binding sites– were analysed with bedtools (v2.25.0). correlations were calculated using spearman’s rho. beanplots were drawn using the ‘beanplot’ package, the circular charts using the ‘circlize’-package and the sankey-diagram using the ‘rcharts’-package (https://github.com/ramnathv/rcharts). all other figures were produced using custom in-house r-scripts., , electronic […]


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circlize in publications

 (41)
PMCID: 5946446
PMID: 29747587
DOI: 10.1186/s12864-018-4738-2

[…] pairs enriched for ligands and receptors in the cumulus-oocyte complexes. we conducted tests of go enrichment with ligands following the procedures described above, and we drew circle plots with the circlize package []., to achieve robust functional annotation of variable genes, we retained only those genes that were detected in all 16 oocytes (n = 6701) or all 16 outercc samples (n = 7168). […]

PMCID: 5943310
PMID: 29743617
DOI: 10.1038/s41598-018-25463-z

[…] genes and to identify potential start and stop codons in the flanking regions of predicted genes. based on annotation features, multiple circular mitogenome maps were drawn using the r package circlize,., two methods, de novo assembly and mapping reads to reference b. glabrata bbo2 rdna, were used for assembly. annotation of gene segment of nuclear rdna that consists of 18s, its1, 5.8s, […]

PMCID: 5901983
PMID: 29659634
DOI: 10.1371/journal.pone.0195974

[…] peach bhlh genes were downloaded from the phytozome database (https://phytozome.jgi.doe.gov/pz/portal.html#). the distribution of each gene on the eight chromosomes of peach was visualized using the circlize software package in r. the start and end positions of each bhlh member on each chromosome in arabidopsis were obtained from the tair database. the orthologous bhlh genes between peach […]

PMCID: 5899322
PMID: 29653584
DOI: 10.1186/s13073-018-0534-5

[…] retained regions (bh-corrected p value < 0.05). the r code used for the integrated analysis is included in additional file . the circular visualization plot was constructed using the r package circlize []., to screen for functional networks among the differentially methylated and expressed genes (conv-r versus gf) we employed the functional networks of tissues in mouse [] prediction tool […]

PMCID: 5896245
PMID: 29634948
DOI: 10.1016/j.ccell.2018.03.013

[…] a lineage respectively, together with <3 supporting reads in all other samples combined., circos plots of the set of svs that were not detected in the normal panel are displayed in b using the r circlize package ()., exact breakpoint types and corresponding single-base resolution were reconstructed through an in-house analysis pipeline centered around the tigra assembler (). briefly, […]


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circlize institution(s)
Division of Theoretical Bioinformatics, German Cancer Research Center (DKFZ), Heidelberg Center for Personalized Oncology (DKFZ-HIPO) and Department for Bioinformatics and Functional Genomics, Institute for Pharmacy and Molecular Biotechnology (IPMB) and BioQuant Center, Heidelberg University, Heidelberg, Germany
circlize funding source(s)
Supported by DKFZ-Heidelberg Center for Personalized Oncology (DKFZ-HIPO).

circlize review

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Anamaria Elek

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Desktop
Circos is an excellent way to visualise large amount of data, and I find circlize to be the best interface for making these plots in R, because it is most adaptable among the several existing packages with the same purpose.