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.
An example usage is:
$ chicPlotViewpoint –interactionFile viewpoint1.txt viewpoint2.txt –range 500000 500000 –backgroundModelFile background_model.txt –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.txt –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 ...]]
[--plotSignificantInteractions]
[--outputFolder OUTPUTFOLDER]
[--outputFormat OUTPUTFORMAT] [--dpi DPI]
[--binResolution BINRESOLUTION]
[--colorMapPvalue COLORMAPPVALUE]
[--maxPValue MAXPVALUE] [--minPValue MINPVALUE]
[--pValue]
[--pValueSignificanceLevels PVALUESIGNIFICANCELEVELS [PVALUESIGNIFICANCELEVELS ...]]
[--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
- --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.
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. Applies only for batch mode.
Default: “.”
- --differentialTestResult, -dif
Path to the H0 rejected files to highlight the regions in the plot.
- --significantInteractionFileFolder, -siff
Folder where the files with detected significant interactions are stored. Applies only for batch mode.
Default: “.”
- --differentialTestResultsFolder, -diff
Folder where the H0 rejected files are stored. Applies only for batch mode.
Default: “.”
- --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
- --outputFolder, -of
Output folder of the files.
Default: “.”
- --outputFormat, -format
Output format of the plot.
Default: “png”
- --dpi
Optional parameter: Resolution for the image, ifoutput is a raster graphics image (e.g png, jpg)
Default: 300
- --binResolution, -r
Resolution of the bin in genomic units. Values are set as number of bases, e.g. 1000 for a 1kb, 5000 for a 5kb or 10000 for a 10kb resolution.
Default: 1000
- --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”
- --maxPValue, -map
Maximal value for p-value. Values above this threshold are set to this value.
- --minPValue, -mp
Minimal value for p-value. Values below this threshold are set to this value.
- --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.
- --outFileName, -o
File name to save the image. 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 (uses the python multiprocessing module).
Default: 4
- --version
show program’s version number and exit