chicPlotViewpoint (version 3.7.2+galaxy0)

Interaction file order:

Rejected H0 file order:

Significant file order:

Plot significant interactions:

Select if the significant regions should be highlighted in the plot. If not set, the significant file data is used only to update the p-values.

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

Combination mode for the plots:

Max p-value:

Maximum value of the plotted p-value.

Min p-value:

Minimum value of the plotted p-value.

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.

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 interactions.hdf5 --range 500000 500000 --backgroundModelFile background_model.txt --pValue --outFileName viewpoint1_2.tar.gz --dpi 300

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