chicPlotViewpoint (version 3.6+galaxy1)

Compute files individually or in batch mode:

Interaction files:

Rejected H0 files:

Significant interaction files:

Upstream range:

Defines the region upstream of a reference point which should be considered in the analysis.

Downstream range:

Defines the region upstream of a reference point which should be considered in the analysis.

Background model:

The background file computed by chicViewpointBackgroundModel

Compute files individually or in batch mode:

Max p-value:

Maximum value of the plotted p-value.

Min p-value:

Minimum value of the plotted p-value.

Resolution of cHi-C data:

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.

Plot p-values as a colorbar:

Color map to use for the heatmap:

Available color map names can be found here: https://matplotlib.org/examples/color/colormaps_reference.html

X-fold mean background:

Plot x-fold region for the mean background.

Image output format:

DPI for image:

Change the default resolution of the plot.

Color list:

Colorlist for the viewpoint lines. For all available colors please check matplotlib documentation: https://matplotlib.org/stable/gallery/color/named_colors.html

Truncate zeros by setting them to one.:

Sets all p-values which are equal to zero to one. This has the effect that the associated positions are not disturbing the presenation of small p-values.

tar output to one file:

The output is tarred to one file and not written to a collection. Set this option if the number of files is large.

Plot of viewpoints

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.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

For more information about HiCExplorer please consider our documentation on readthedocs.io