hicCorrelate

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 ...]] [--version]
optional 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.
--method=pearson
 

Correlation method to use.

Possible choices: pearson, spearman

--log1p=False 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.
--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.
--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
--colorMap=jet Color map to use for the heatmap. Available values can be seen here: http://matplotlib.org/examples/color/colormaps_reference.html
--plotFileFormat
 

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.

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

--plotNumbers=False
 If set, then the correlation number is plotted on top of the heatmap.