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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

Type parameters (generics)

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.

Outputs

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.

Test cases

Test case Parameters IN
data
IN
data2
IN
data3
IN
data4
IN
data5
IN
data6
IN
data7
IN
data8
IN
data9
IN
data10
IN
data11
IN
dataAnnotation
IN
plotAnnotation
IN
links
IN
highlights
IN
plotParams
IN
karyotype
OUT
circos
OUT
ideogram
OUT
ticks
OUT
plot
case1 properties data data2 data3 (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) links highlights (missing) (missing) (missing) (missing) (missing) (missing)

circosCom = circos,
drawGrid = true,
min = 0.0,
max = 5.0,
autoYScale=false,
plotScale=0.65,0.9,0.65,0.9,0.65,0.9

case2 properties data (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) plotAnnotation (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing)

chr = hs1

case3 properties data data2 data3 (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) (missing) links highlights plotParams (missing) (missing) (missing) (missing) (missing)

circosCom = circos,
drawGrid = true,
min = 0.0,
max = 5.0,
autoYScale=false,
plotScale=0.65,0.9,0.65,0.9,0.65,0.9


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