chicPlotViewpoint¶
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]
[--plotSignificantInteractions]
[--outFileName OUTFILENAME]
[--outputFormat OUTPUTFORMAT] [--dpi DPI]
[--combinationMode {dual,single,allGenes,oneGene}]
[--combinationName COMBINATIONNAME]
[--colorMapPvalue COLORMAPPVALUE]
[--maxPValue MAXPVALUE] [--minPValue MINPVALUE]
[--pValue]
[--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
- --range
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”
- --dpi
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).
- --colorMapPvalue
Color map to use for the p-value. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html (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
- --version
show program’s version number and exit