shinyCircos: an R/Shiny application for interactive creation of Circos plot

About

Upload data for inner tracks

Data of zero or more tracks can be uploaded. For now, a maximum of 10 tracks are allowed. For any track, the first three columns of the uploaded data should be chromosome ID, the start and end coordinates of genomic regions. For plot of point, line and bar, the uploaded data can contain one or more columns to indicate the 'color', 'cex' or 'pch' used in the plot. 'cex' is used to control the size of data points while 'pch' is used to specify the symbols used in plot of point. See example data for more details.


Upload data to create links

Data to create links between different genomic regions should be composed of 6 or 7 columns. The first three columns of each row represent the coordinate of a genomic region while the 4th to 6th columns of each row represent the coordinate of another genomic region. For data with 7 columns, the 7th column should be categorical characters indicating varying colors or numbers indicating gradual colors used for different links. The name of the 7th column should be 'color'. A link will be created between the two genomic regions in each row. See example data for more details.


Data uploaded should use any of the separator in the set [,\t |;:].


Plot options

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four columns separated by commas indicating the chromosome ID, start coordinate, end coordinate and specified color. For example, 'chr1,1,100000000,red'. Hex color codes like '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.

Data color

For data with 'color' column indicated by numbers, links are filled with colors specified by the user.

Low Color

Middle Color

High Color


Paste data below:

Each row should contain four components separated by commas including the chromosome ID, start coordinate, end coordinate and the specified color. For example, 'chr1,1,100000000,red'. Hex color codes as '#FF0000' are also supported.


Data separated by commas.


Gallery

Help

  • Software references
  • 1. R Development Core Team. R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna (2016)
    2. RStudio and Inc. shiny: Web Application Framework for R. R package version 1.0.0 (2016)
    3. Gu, Z. circlize: Circular Visualization. R package version 0.4.1 (2017)
    4. Neuwirth, E. RColorBrewer: ColorBrewer palettes. R package version 1.1-2 (2014)
    5. Lawrence, M. GenomicRanges: Representation and manipulation of genomic intervals and variables defined along a genome. R package version 1.24.3 (2016)
    6. Dowle, M. data.table: Extension of Data.frame. R package version 1.9.6 (2015)
    7. Burow, C. RLumShiny: "Shiny" Applications for the R Package "Luminescence". R package version 0.1.1 (2016)
    8. R Core Team and contributors worldwide. grDevices: Graphics devices and support for base and grid graphics. R package version 3.3.3 (2016)

  • Further references
  • This application was created by Wen Yao and Yiming Yu . Please send bugs and feature requests to Wen Yao (ywhzau at gmail.com) or Yiming Yu (yimingyyu at gmail.com). This application uses the shiny package from RStudio .

  • Please cite
  • Yiming Yu, Yidan Ouyang, and Wen Yao. shinyCircos: an R/Shiny application for interactive creation of Circos plot. Bioinformatics. 2017 Nov. 24. doi:10.1093/bioinformatics/btx763

  • !!Note!!
  • Users are encouraged to install and use shinyCircos on local personal computers. Please check the help menu of the shinyCircos application or https://github.com/venyao/shinyCircos for the installation of shinyCircos on local computers.