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

usage: chicPlotViewpoint --interactionFile INTERACTIONFILE --range RANGE RANGE
                         [--backgroundModelFile BACKGROUNDMODELFILE]
                         [--differentialTestResult DIFFERENTIALTESTRESULT]
                         [--significantInteractions SIGNIFICANTINTERACTIONS]
                         [--outFileName OUTFILENAME]
                         [--outputFormat OUTPUTFORMAT] [--dpi DPI]
                         [--combinationMode {dual,single,allGenes,oneGene}]
                         [--combinationName COMBINATIONNAME]
                         [--colorMapPvalue COLORMAPPVALUE]
                         [--maxPValue MAXPVALUE] [--minPValue MINPVALUE]
                         [--pValueSignificanceLevels PVALUESIGNIFICANCELEVELS [PVALUESIGNIFICANCELEVELS ...]]
                         [--xFold XFOLD] [--truncateZeroPvalues]
                         [--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.

Optional arguments

--backgroundModelFile, -bmf

path to the background file which should be used for plotting

--differentialTestResult, -dif

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

--significantInteractions, -si

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

--plotSignificantInteractions, -psi

Highlights the significant interactions in the plot itself. If not set, only the p-values are updated

Default: False

--outFileName, -o

Output tar.gz of the files (Default: “plots.tar.gz”).

Default: “plots.tar.gz”

--outputFormat, -format

Output format of the plot (Default: “png”).

Default: “png”


Optional parameter: Resolution for the image, ifoutput is a raster graphics image (e.g png, jpg) (Default: 300).

Default: 300

--combinationMode, -cm

Possible choices: dual, single, allGenes, oneGene

This option defines how the interaction data should be computed and combined: dual: Combines as follows: [[matrix1_gene1, matrix2_gene1], [matrix2_gene1, matrix3_gene1],[matrix1_gene2, matrix2_gene2], …]single: Combines as follows: [matrix1_gene1, matrix1_gene2, matrix2_gene1, …], allGenes: Combines as follows: [[matrix1_gene1, matrix2_gene1, matrix2_gene1], [matrix1_gene2, matrix2_gene2, matrix3_gene2], …]oneGene: Computes all data of one gene, please specify ‘–’. If a gene is not unique, each viewpoint is treated independently. (Default: “dual”).

Default: “dual”

--combinationName, -cn

Gene name or file name for modes ‘oneGene’ or ‘file’ of parameter ‘–combinationMode’ (Default: None).


Color map to use for the p-value. Available values can be seen here: (Default: “RdYlBu”).

Default: “RdYlBu”

--maxPValue, -map

Maximal value for p-value. Values above this threshold are set to this value (Default: 0.1).

Default: 0.1

--minPValue, -mp

Minimal value for p-value. Values below this threshold are set to this value (Default: 0.0).

Default: 0.0

--pValue, -p

Plot p-values as a colorbar

Default: False

--pValueSignificanceLevels, -psl

Highlight the p-values by the defined significance levels.

--xFold, -xf

Plot x-fold region for the mean background.

--truncateZeroPvalues, -tzpv

Sets all p-values which are equal to zero to one.

Default: False

--colorList, -cl

Colorlist for the viewpoint lines (Default g b c m y k).

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

--threads, -t

Number of threads (uses the python multiprocessing module) (Default: 4).

Default: 4


show program’s version number and exit