演示文稿 Shiny Circos Help Manual

shinyCircos_Help_Manual

shinyCircos_Help_Manual

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shinyCircos
an R/Shiny application for interactive creation of

Circos plot

Yiming Yu1, Yidan Ouyang1,*, Wen Yao1,2*
1National

Key Laboratory of Crop Genetic Improvement, National Center of

Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan
430070, China, 2College of Life Science and Technology, Henan Agricultural
University, Zhengzhou 450002, China.
Contact: yaowen@henau.edu.cn, diana1983941@mail.hzau.edu.cn

The source code of shinyCircos is deposited in
Github (https://github.com/venyao/shinyCircos).
shinyCircos is deployed at https://yimingyu.shinyapps.io/shinycircos/
and http://shinycircos.ncpgr.cn/. Users can use shinyCircos online by
accessing either of the two URLs.

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.

1. Interface of shinyCircos

Menu in shinyCircos: About
 The shinyCircos application contains five menus, “About”, “Data upload”,
“Circos visualization”, “Gallery” and “Help”.

 The “About” menu lists the R packages used in shinyCircos.

Menu in shinyCircos: Data upload
Download
example data

View uploaded data

Upload data
 The “Data upload” menu allows uploading of input data for Circos plots.
 A glimpse of the uploaded data will be printed on this page.
 Example datasets could be downloaded from this menu.

Menu in shinyCircos: Circos visualization
Download
figures

Download
scripts

Show Pictures

Tune
plot
options
 After data uploading, the “Circos visualization” menu allows generation of Circos
plot.
 Various options are provided to tune the appearance of the Circos plot.

Menu in shinyCircos: Gallery

 Fifty example figures generated by shinyCircos are listed in the “Gallery” menu.

Menu in shinyCircos: Help

Download this manual for
the usage of shinyCircos

 Instructions for installation of shinyCircos on local computers or web servers
are shown in the “Help” menu.

2. Usage of shinyCircos

Step 1: Data uploading
1.1 Upload chromosome data

1.2 Upload track data

 Data from 0 to 10 tracks can be uploaded.
 The first 3 columns of the uploaded data
should be the chromosome ID, the start
and end coordinates of genomic regions.

1.3 Complete uploading

Step 2: Circos visualization
2.1 Turn to “Circos visualization” menu

2.4 Download figures

2.5 Download scripts

 The chromosome data is compulsory and
defines the frame of a Circos plot.
2.2 Tune plot options
2.3 Make the plot

 Please click the “Go!” button if any
options are modified.

2.1 Plot chromosomes

Upload chromosome data

Click “Browse” to select file

 Use the “Data upload” menu for data input.
 Chromosome data can be either chromosome ideograms (“Cytoband” type, see
example data “chromosome_cytoband.csv” for detail) or simple definition of
chromosome lengths (“General” type, see example data “chromosome_general.csv”
for detail).

Options

Add color band for chromosomes.
Colors for chromosome/sector.
Add labels on the outermost circle.
Add size units of genomic regions on the chromosome axis.
Gap width between neighboring sectors.
The text to appear in the legend.

Example 1

Data format
Chromosome data: chromosome_general.csv
Data type: General

Example 2

Data format

Chromosome data: chromosome_cytoband.csv
Data type: Cytoband

2.2 Plot points

Upload point data

Select “Upload”
Select file
Select plot type “point”

Options

The color used for data plotting can be randomly assigned by the application or
specified by the users.
A decimal number in [0, 1] to adjust the color transparency.
Decimal numbers in [0, 1] to adjust the y axis coordinates of baselines.
The color used for baselines.
The color for the background.
Height of the track.
Margin size of the track.
Add borders to the different chromosome sectors.

Options
Genomic regions can be highlighted with specified colors.

Each row should contain four components separated by commas including the
chromosome ID, start coordinate, end coordinate and the specified color.

A decimal number in [0, 1] to adjust the color transparency for the highlighted
regions.

Example 1
Data format
Any track can be used
for data uploading.

 Simplest data to plot point should contain at least 4 columns including the
chromosome ID, start coordinate, end coordinate and multiple columns of values.

Example 2
Data format
 The last column “pch’’ indicates
different point types for differing
point_pch.csv
data groups.

 The last column “color’’ indicates
point_color.csv different colors for differing data
groups.

 The last columns “color’’ and “pch”
point_color_pch.csv represent different colors and
point types for different data
groups.

Example 3
Data format

point_cex.csv

point_color_cex.csv

point_pch_cex.csv

point_color_pch_cex.csv

 The “cex” column is a numeric vector represents different point size.

Example 4
Data format

stack_point.csv
 The last column “stack” is a numeric vector or a character vector.
 In stack mode, the y-axis is split into several bins with equal height and all data
points are put onto different “horizontal” bins based on the “stack” column.

2.3 Plot lines

Options

Fill the area below the lines.
Filled the area with color, which can be identical to line color
or specified by the user.

 See section 2.2 for more plot options.

Example 1
Data format

line.csv

line_multicolumn.csv

 Simplest data to plot line should contain at least 4 columns including the
chromosome ID, start coordinate, end coordinate and multiple columns of values.

Example 2
Data format

stack_line.csv

line_color.csv

2.4 Plot bars

Options

Bars can be unidirectional or bidirectional. For bidirectional bars,
the 4th column with data values will be divided into two groups
based on the boundary value.

Color for the outer bars.
Color for the inner bars.

 See section 2.2 for more plot options.

Example 1
Data format
barplot.csv

barplot_color.csv

 Data for bar plot generally includes 4 columns.
 The 4th column is a numeric vector.
 A “color” column can be added to assign color to different bars.

Example 2
Data format

barplot.csv

barplot_bidirectional.csv

 For bidirectional bars, each genomic region corresponds to one or two values.

2.5 Plot rects

Upload rect data
Data format

rect_gradual.csv

 Data for rect plot generally includes four
columns.
 The last column should be a numeric vector
representing gradual values or a character
vector representing discrete variables.

rect_discrete.csv

Options

The rects are filled with gradual or discrete colors.
The color used in data plotting can be randomly assigned by the
application or specified by the users.

 See section 2.2 for more plot options.

2.6 Plot heatmaps

Options

Colors used for the heatmap.

Add genomic position lines between tracks.
Height of the position lines.
Margin size of the position lines.

 See section 2.2 for more plot options.

Add borders to heatmap grids.
The color used for the borders of heatmap grids.

Upload heatmap data
Data format

heatmap.csv
 Apart from the first three columns, other columns are numeric vectors
representing different values.

2.7 Plot ideogram

Upload ideogram data
Data format

point.csv

chromosome_ideogram.csv

 Data to plot ideogram is the same as “chromosome_cytoband.csv”.
 Ideogram plot can be generated in any track.

2.8 Plot labels

Upload label data

Options

Add labels to mark genes or genomic regions for this track using
data uploaded in the “Data upload” menu.
Specify labels positions relative to the track.
Height of the labels.
Margin size of the labels.

 See section 2.2 for more plot options.

2.9 Plot links

Upload links data

Data to plot links should include 6 or 7 columns.

Select “Links data” and upload file.

Example 1
Data format

links.csv
 Data with 6 columns.
 Columns 1-3 and columns 4-6 represent the two ends of connectors respectively.

Example 2
Data format

links_color.csv

 Data with 7 columns.
 A “color” column representing different groups of data with differing colors can
be added.

3. Other features

3.1 Figure size

Options

Users can adjust the height and width
of the Circos plot.
The figure size in both the browser and the
download files would be affected.

3.2 Font size

Options

The font size can be ‘small’, ‘medium’, ‘large’ or specified by the user.

3.3 Legend

Options

Legend can be added at the right or the center of the Circos plot.

Input
legend text

Legend option

Input
legend text

Legend option
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