chicPlotViewpoint plots one or many viewpoints with the average background model and the computed p-value per sample. Moreover it can highlight differential interactions of two samples and or significant regions.

An example usage is:

$ chicPlotViewpoint –interactionFile viewpoint1.bed viewpoint2.bed –range 500000 500000 –backgroundModelFile background_model.bed –pValue –outFileName viewpoint1_2.png –dpi 300

In batch mode the list of file names and the folders containing the files need to be given:

$ chicPlotViewpoint –interactionFile viewpoint_names.txt -interactionFileFolder viewpointFilesFolder –differentialTestResult rejected_H0.txt –differentialTestResultsFolder differentialFolder –range 500000 500000 –backgroundModelFile background_model.bed –pValue –outputFolder plotsFOlder –dpi 300 –threads 20

usage: chicPlotViewpoint --interactionFile INTERACTIONFILE
                         [INTERACTIONFILE ...] --range RANGE RANGE
                         [--backgroundModelFile BACKGROUNDMODELFILE]
                         [--interactionFileFolder INTERACTIONFILEFOLDER]
                         [--differentialTestResult DIFFERENTIALTESTRESULT [DIFFERENTIALTESTRESULT ...]]
                         [--significantInteractionFileFolder SIGNIFICANTINTERACTIONFILEFOLDER]
                         [--differentialTestResultsFolder DIFFERENTIALTESTRESULTSFOLDER]
                         [--significantInteractions SIGNIFICANTINTERACTIONS [SIGNIFICANTINTERACTIONS ...]]
                         [--outputFolder OUTPUTFOLDER]
                         [--outputFormat OUTPUTFORMAT] [--dpi DPI]
                         [--binResolution BINRESOLUTION]
                         [--colorMapPvalue COLORMAPPVALUE]
                         [--maxPValue MAXPVALUE] [--minPValue MINPVALUE]
                         [--pValue] [--xFold XFOLD]
                         [--outFileName OUTFILENAME] [--batchMode]
                         [--plotSampleNumber PLOTSAMPLENUMBER]
                         [--colorList COLORLIST [COLORLIST ...]]
                         [--threads THREADS] [--help] [--version]

Required arguments

--interactionFile, -if

path to the interaction files which should be used for plotting


Defines the region upstream and downstream of a reference point which should be included. Format is –region upstream downstream e.g.: –region 500000 500000 plots 500kb up- and 500kb downstream. This value should not exceed the range used in the other chic-tools.

Default: [500000, 500000]

Optional arguments

--backgroundModelFile, -bmf

path to the background file which should be used for plotting

--interactionFileFolder, -iff

Folder where the interaction files are stored in. Applies only for batch mode.

Default: “.”

--differentialTestResult, -dif

Path to the files which with the H0 rejected files to highlight the regions in the plot.

--significantInteractionFileFolder, -siff

Folder where the detected significant interactions files are stored in. Applies only for batch mode.

Default: “.”

--differentialTestResultsFolder, -diff

Folder where the H0 rejected files are stored in. Applies only for batch mode.

Default: “.”

--significantInteractions, -si

Path to the files which detected significant interactions to highlight the regions in the plot.

--outputFolder, -of

Output folder of the files.

Default: “.”

--outputFormat, -format

Output format of the plot.

Default: “png”


Optional parameter: Resolution for the image in case theoutput is a raster graphics image (e.g png, jpg)

Default: 300

--binResolution, -r

Resolution of the bin in genomic units. Values are usually e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.

Default: 1000


Color map to use for the p-value. Available values can be seen here:

Default: “RdYlBu”

--maxPValue, -map

Maximal value for p-value. Values above are set to this value.

--minPValue, -mp

Minimal value for p-value. Values below are set to this value.

--pValue, -p

Plot p-values as a colorbar

Default: False

--xFold, -xf

Plot x-fold region for the mean background.

--outFileName, -o

File name to save the image. It is not used in batch mode.

--batchMode, -bm

The given file for –interactionFile and or –targetFile contain a list of the to be processed files.

Default: False

--plotSampleNumber, -psn

Number of samples per plot. Applies only in batch mode.

Default: 2

--colorList, -cl

Colorlist for the viewpoint lines.

Default: [‘g’, ‘b’, ‘c’, ‘m’, ‘y’, ‘k’]

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4


show program’s version number and exit