Component: CircosPlot

CircosPlot

Draws circos plots from genomic data. Circos plots are created by the circos perl library.

If dataAnnotation input is defined, the input data is assumed to be strictly numeric with an id row. If not, then the input is assumed to contain an id, start and end coordinates columns followed by n rows of numeric data.

Column names in the input files are removed by the component prior to launching circos.

The karyotype of a species can be specified as an input. The latest human genome build is included in the component by default.

Version	0.7
Bundle	microarray
Categories	Plot
Specialties	generic
Authors	Riku Louhimo (Riku.Louhimo@Helsinki.FI), Sirkku Karinen (sirkku.karinen@helsinki.fi)
Issue tracker	View/Report issues
Requires	Asser.jar (jar) ; circos (circos-0.52 or newer)
Source files	component.xml CircosPlot.java
Usage	Example with default values CircosPlot( data = CSV, //data2 = CSV, //data3 = CSV, //data4 = CSV, //data5 = CSV, //data6 = CSV, //data7 = CSV, //data8 = CSV, //data9 = CSV, //data10 = CSV, //data11 = CSV, //dataAnnotation = CSV, //plotAnnotation = CSV, //links = CSV, //highlights = CSV, //plotParams = T, //karyotype = T, alternateColors = false, autoYScale = true, chr = "", chrScale = "", circosCom = "circos", circosLibrary = "", commonYScale = true, drawBands = false, drawGrid = false, fontSize = 24, max = 5.0, min = 0.0, plotScale = "constant=0.1", plotType = "scatter", radius = 0.5, showAxis = false )

Version

0.7

Bundle

microarray

Categories

Plot

Specialties

generic

Authors

Riku Louhimo (Riku.Louhimo@Helsinki.FI), Sirkku Karinen (sirkku.karinen@helsinki.fi)

Issue tracker

View/Report issues

Requires

Asser.jar (jar) ; circos (circos-0.52 or newer)

Source files

component.xml CircosPlot.java

Usage

Example with default values

Inputs

Name	Type	Mandatory	Description
data	CSV	Mandatory	Data that is plotted. Data can have column names but they are ignored. Data must contain columns chrID, start, end and value (in this order). chrID values must match chrID values in the karyotype file - defaults are of the form chr1, chr2, etc. If the dataAnnotation input is connected, data is assumed to contain a rowID and a value column.
data2	CSV	Optional
data3	CSV	Optional
data4	CSV	Optional
data5	CSV	Optional
data6	CSV	Optional
data7	CSV	Optional
data8	CSV	Optional
data9	CSV	Optional
data10	CSV	Optional
data11	CSV	Optional
dataAnnotation	CSV	Optional	Optional annotation table for the data containing RowID, chrID, start and end coordinates. See also data input.
plotAnnotation	CSV	Optional	Additional annotation that will be inserted into the plot e.g., gene names.
links	CSV	Optional	Contains links between genomic loci. Each row contains a linkID, chrID, start and end coordinates and an optional link-specific field. chrID must match chrIDs in the karyotype file. Each linkID consists of two parts: 'link'+ID e.g., "link00010". A linkID must be found twice in the links file, once for the link start locus and once for end locus. The ID part must be unique for a link pair.
highlights	CSV	Optional	Plot highlight blocks. Each row contains chrID, start and end coordinates. An additional column can be included to override default parameters (e.g., fill_color=yellow).
plotParams	T (generic)	Optional	Optional input containing a circos plot configuration file. The contents of this input are catenated to the circos plot configuration without checks. Please refer to the circos plot user guide for syntax.
karyotype	T (generic)	Optional	Human karyotype file. If not included, the default karyotype without chromosome bands will be used. The karyotype coordinates come from human genome build 38 also known as GRch38.

Name

Type

Mandatory

Description

data

CSV

Mandatory

Data that is plotted. Data can have column names but they are ignored. Data must contain columns chrID, start, end and value (in this order). chrID values must match chrID values in the karyotype file - defaults are of the form chr1, chr2, etc. If the dataAnnotation input is connected, data is assumed to contain a rowID and a value column.

data2

CSV

Optional

data3

CSV

Optional

data4

CSV

Optional

data5

CSV

Optional

data6

CSV

Optional

data7

CSV

Optional

data8

CSV

Optional

data9

CSV

Optional

data10

CSV

Optional

data11

CSV

Optional

dataAnnotation

CSV

Optional

Optional annotation table for the data containing RowID, chrID, start and end coordinates. See also data input.

plotAnnotation

CSV

Optional

Additional annotation that will be inserted into the plot e.g., gene names.

links

CSV

Optional

Contains links between genomic loci. Each row contains a linkID, chrID, start and end coordinates and an optional link-specific field. chrID must match chrIDs in the karyotype file. Each linkID consists of two parts: 'link'+ID e.g., "link00010". A linkID must be found twice in the links file, once for the link start locus and once for end locus. The ID part must be unique for a link pair.

highlights

CSV

Optional

Plot highlight blocks. Each row contains chrID, start and end coordinates. An additional column can be included to override default parameters (e.g., fill_color=yellow).

plotParams

T (generic)

Optional

Optional input containing a circos plot configuration file. The contents of this input are catenated to the circos plot configuration without checks. Please refer to the circos plot user guide for syntax.

karyotype

T (generic)

Optional

Human karyotype file. If not included, the default karyotype without chromosome bands will be used. The karyotype coordinates come from human genome build 38 also known as GRch38.

Name	Type	Description
circos	T (generic)
ideogram	T (generic)
ticks	T (generic)
plot	Latex

Name

Type

Description

circos

T (generic)

ideogram

T (generic)

ticks

T (generic)

plot

Latex

Parameters

Name	Type	Default	Description
alternateColors	boolean	false	Use a predefined set of alternating colors when drawing data points.
autoYScale	boolean	true	Automatically scans through all data files and finds the upper and lower limits.
chr	string	""	Comma separated list of chromosome names which indicates which chromosomes to plot. The empty default plots all. The chromosome names (chrID) here must match the chrID in the input data and karyotype files.
chrScale	string	""	Comma separated list of chromosome names which indicate the relative scale of a chromosome e.g., 'chr1=5,chr3=0.2'.
circosCom	string	"circos"	System specific circos command.
circosLibrary	string	""	Optional directory of circos include files. Default searches the 'etc' directory under system specific circos installation.
commonYScale	boolean	true	Use common scale for all plots, or find automatically the scale for each data file.
drawBands	boolean	false	Turns on chromosomal bands.
drawGrid	boolean	false	Turns on grid underlying data.
fontSize	int	24	Font size for 'plotAnnotation' labels.
max	float	5.0	Y-scale maximum for plots.
min	float	0.0	Y-scale minimum for plots.
plotScale	string	"constant=0.1"	Defines how plots are placed into circle (constant=0.1/relative/0.1,0.5,0.8) : a) Constant spacing starting from 0.9 EXAMPLE constant=0.2 creates 0.9,0.7,0.5,... b) Space is divided for all the plots c) Comma separated list of plot positions e.g., 0.9,0.8,0.6,0.55 creates first plot from 0.9 to 0.8, next from 0.6 to 0.55
plotType	string	"scatter"	Type of the plots. Values = scatter/line/histogram/tile.
radius	float	0.5	Radius value for links.
showAxis	boolean	false	Draws a set of y-axis grid lines within plot tracks.

Name

Type

Default

Description

alternateColors

boolean

false

Use a predefined set of alternating colors when drawing data points.

autoYScale

boolean

true

Automatically scans through all data files and finds the upper and lower limits.

chr

string

Comma separated list of chromosome names which indicates which chromosomes to plot. The empty default plots all. The chromosome names (chrID) here must match the chrID in the input data and karyotype files.

chrScale

string

Comma separated list of chromosome names which indicate the relative scale of a chromosome e.g., 'chr1=5,chr3=0.2'.

circosCom

string

"circos"

System specific circos command.

circosLibrary

string

Optional directory of circos include files. Default searches the 'etc' directory under system specific circos installation.

commonYScale

boolean

true

Use common scale for all plots, or find automatically the scale for each data file.

drawBands

boolean

false

Turns on chromosomal bands.

drawGrid

boolean

false

Turns on grid underlying data.

fontSize

int

Font size for 'plotAnnotation' labels.

max

float

5.0

Y-scale maximum for plots.

min

float

0.0

Y-scale minimum for plots.

plotScale

string

"constant=0.1"

Defines how plots are placed into circle (constant=0.1/relative/0.1,0.5,0.8) : a) Constant spacing starting from 0.9 EXAMPLE constant=0.2 creates 0.9,0.7,0.5,... b) Space is divided for all the plots c) Comma separated list of plot positions e.g., 0.9,0.8,0.6,0.55 creates first plot from 0.9 to 0.8, next from 0.6 to 0.55

plotType

string

"scatter"

Type of the plots. Values = scatter/line/histogram/tile.

radius

float

0.5

Radius value for links.

showAxis

boolean

false

Draws a set of y-axis grid lines within plot tracks.