Computes pairwise correlations between Hi-C matrices data. The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.

usage: hicCorrelate [-h] [--zMin ZMIN] [--zMax ZMAX] [--colorMap]
                    [--plotFileFormat FILETYPE] [--plotNumbers] --matrices
                    MATRICES [MATRICES ...] [--method {pearson,spearman}]
                    [--log1p] [--labels sample1 sample2 [sample1 sample2 ...]]
                    [--range RANGE] --outFileNameHeatmap OUTFILENAMEHEATMAP
                    --outFileNameScatter OUTFILENAMESCATTER
                    [--chromosomes CHROMOSOMES [CHROMOSOMES ...]]
                    [--threads THREADS] [--version]

Named Arguments

–matrices, -m Matrices to correlate (usually .h5 but other formats are allowed). hicCorrelate is better used on un-corrected matrices in order to exclude any changes introduced by the correction.

Possible choices: pearson, spearman

Correlation method to use.

Default: “pearson”


If set, then the log1p of the matrix values is used. This parameter has no effect for Spearman correlations but changes the output of Pearson correlation and, for the scatter plot, if set, the visualization of the values is easier.

Default: False

–labels, -l User defined labels instead of default labels from file names. Multiple labels have to be separated by space, e.g. –labels sample1 sample2 sample3
–range In bp with the format low_range:high_range, for example 1000000:2000000. If –range is given only counts within the range are considered.
–outFileNameHeatmap, -oh
 File name to save the resulting heatmap plot
–outFileNameScatter, -os
 File name to save the resulting scatter plot
–chromosomes List of chromosomes to be included in the correlation.

Number of threads. Using the python multiprocessing module. Is only used with ‘cool’ matrix format. One master process which is used to read the input file into the buffer and one process which is merging the output bam files of the processes into one output bam file. All other threads do the actual computation.

Default: 4

–version show program’s version number and exit

Heat map options

–zMin, -min Minimum value for the heat map intensities. If not specified the value is set automatically
–zMax, -max Maximum value for the heat map intensities.If not specified the value is set automatically

Color map to use for the heatmap. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html

Default: “jet”


Possible choices: png, pdf, svg, eps, emf

Image format type. If given, this option overrides the image format based on the plotFile ending. The available options are: png, emf, eps, pdf and svg.


If set, then the correlation number is plotted on top of the heatmap.

Default: False