Plotting genes

A new feature to plot genes in UCSC genome browser format within the
visualized area.

parameters:

-g (--plotGenes): a sorted bed file with gene names should be provided.
-gl (--geneLabels): a boolean to make gene names visible (default) or
not.

Special thanks to Harris Lazaris for his suggestions.

A new parameter for determining heatmap range of comparison plots:

-ce (--compareEx): comma separated two absolute values (such as for -4
to 6: 4,6)

Manual Update

Version 0.6.05.compare

New parameters:

-dc to assign custom colors to domain plots.
-ext to determine output file format (pdf/tiff/svg).

Underdevelopment feature: log2 comparison of first two matrices. (use
with -c 1)

HiCPlotter version 0.5.1

A manual is now available for HiCPlotter parameters.

Epilogos plotting:
HiCPlotter can now visualize Hi-C data with Epilogos
(http://compbio.mit.edu/epilogos/#) from Kellis lab. Please check the
manual for the parameters.

Whole genome plotting with triple sparse file format is fixed. Please
use -wg parameter with -chr, (-chrY for whole genome interactions,
otherwise enter a particular chromosome name until which interactions
profiles will be plotted). Please check the ReadMe page for examples.

A new parameter (-hc) is introduced to color the area under histograms.
Same as -tc/-ac please provide a hexadecimal number.

ReadMe

Update

examplePlots