Copyright (C) 2007 Free Software Foundation, Inc. https://fsf.org/. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed.

plotHicGenome: the tools are used for displaying hic signal of whole genome

Installation

Python package and command line interface for displaying Hic signals of assembly genome was tested with python 2.7 on linux. You can install it using pip or through source codes.

• Dependent pakages
  matplotlib-2.2.3
  pandas-0.24.0
  numpy-1.16.4
  scipy-1.2.0
  

• Install by pip
  pip install plotHicGenome --user
  

• Install through raw codes
  git clone https://github.com/chenjunhui/plotHicGenome
  cd plotHicGenome
  python setup.py install [--prefix=/user/direction]
  

Notably: you'd better install it under virtual environment in case system conflict.

Create virtualenv refer to: https://docs.python.org/3/tutorial/venv.html.
virtualenv --no-site-packages venv //[project Name]
Finally, you need source venv/activate or . venv/activate, and execute as the methods above.

After completing to install, you can type on the command line:

export PATH="/user/direction/bin:$PATH"
plotHicGenome  --help

USAGE

The package includes two sub-commands {Hicproc, juicer}, and you can choose corresponding module basing on result of the your hic matrix.

/user/direction/bin/plotHicGenome  --help

****
plotHicGenome version: 0.1.0
please chose the plot type, subcommand: juicer or Hicproc,command
plotHicGenome juicer
plotHicGenome Hicproc
****

Display Hic matrix of Hic-proc

plotHicGenome   Hicproc     Hic_500000.matrix   Hic_500000_abs.bed   -p  chr  -W  whole  -E  chr20  -n  40  -r  500000  -l   T   -i  300   -z  6,6   -C  black   -L  1 -A  1  -B  "0.5%" -D 0.1    -F  6  -o  HicprocWhole.pdf    -R  ./
plotHicGenome   Hicproc     Hic_500000.matrix   Hic_500000_abs.bed   -p  chr  -W  chr1  -E  chr20  -n  40  -r  500000  -l   T   -i  300   -z  6,6   -C  black   -L  1 -A  1  -B  "0.5%" -D 0.1    -F  6  -o  Hicprocchr1.pdf    -R  ./

Display Hic matrix of Juicerbox

If run the sub-command firstly, the command will calculate the Hic matrix to produce the Hic matrix and figure. However, if dissatisfied with the produced figure above, the parameters are needed ajusting to obatain a better displaying.

Sorted by chromosome size

plotHicGenome  juicer  ./merged_nodups.txt  ./genome.review.assembly  -W whole -n  24   -s  True  -l  t  -F  4   -r  500000  -X  2  -w  0.5  -d  3  -S  'dashed'  -i 300 -z 6,6  -C  'black'  -L  0.8   -A  0.8  -B  '1%' -D  0.2  -o  Juicerboxsorted.pdf    -R   ./sorted

Non-sorted by chromosome size

plotHicGenome  juicer  ./merged_nodups.txt  ./genome.review.assembly  -W whole -n  24   -s  False  -l  t  -F  4   -r  500000  -X  2  -w  0.5  -d  3  -S  'dashed'  -i 300 -z 6,6  -C  'black'  -L  0.8   -A  0.8  -B  '1%' -D  0.2  -o  JuicerboxNonsorted.pdf    -R   ./sorted

run sub-command juicer secondly

plotHicGenome  juicer  ./merged_nodups.txt  ./genome.review.assembly -W  whole   -n  24   -l  t  -F  4   -r  500000  -X  2  -w  0.5  -d  3  -S  'dashed'  -i 300 -z 6,6  -C  'black'  -L  0.8   -A  0.8  -B  '1%' -D  0.2  -o  JuicerboxNtsortedMtx.pdf  -H  sorted/Hicmatrix.txt   -R   ./sorted

Notably, axesTicks.csv should exist in the ourdir, command read it in default.

Plot single choromosome

plotHicGenome juicer   ./merged_nodups.txt  .genome.review.assembly  -W   chr1   -n  24   -s  True  -l  t  -F  4   -r  500000  -X  2  -w  0.5  -d  3  -S  'dashed'  -i 300 -z 6,6  -C  'black'  -L  0.8   -A  0.8  -B  '1%' -D  0.2  -o  JuicerboxNtsortedMtx_testchr24.pdf  -H  ./sorted/Hicmatrix.txt   -R   ./sorted

Contributors

• chenjhbio chenjunhui@genomics.cn

Parameters

usage: plotHicGenome [-h] [-H MTX] [-p P] [-M CM] [-W CHR] [-E ECHR] [-n N] [-s _SORTED] [-r R] [-l LOG] [-i DPI] [-z FIGS] [-X AXESL] [-w AXESW] [-d AXESPD] [-S GS] [-C COLO][-L WD] [-A AP] [-B CBSZ] [-D CBPD] [-F FZ] [-o FG] [-R ODIR] [-v] {juicer,Hicproc} Hic bed

This kit show links of Hic,you should provide hicfile[sparse matrix of Hic proc | merged_nodups.txt that result from juicer] and bed file [bed file of Hic proc|assemblyView of Juicer], if possible,you may provide chromosome prefix in plot, and default prefix chr.

positional arguments:
{juicer,Hicproc} this is only flag, which remind you to run corresponding module
Hic Result of juicer: //Hic matrix
bed ajusted by juicerbox //bed file

optional arguments:
-h, --help show this help message and exit
-H MTX, --Matrix MTX matrix file including Hic relation of chromosome //Hic matrix [bin]
-p P, --prefix P chr prefix //chromosome prefix
-M CM, --cMap CM color shapping you choseed,five cMap you can select //mapplotlib color map
-W CHR, --chromosome CHR //chromoesome,default: whole plot the whole genome, if you provide the last chomosome, then the figure will show between first chromosome and the last chomosome for Hic matrix of Hicproc method. while you provide single choromosome, it will display the chromosome.
-E ECHR, --endChr ECHR //last chromosome,if plot using Hic matrix of Hicproc method assigned parameter the last chromosome in the bed, the ved file should be ordered,it's only for Hic matrix of Hicproc method.
-n N, --chrNumber N assigned parameter the chromosome number of genome, //chromosome number of genome
it's only for Hic matrix of juicerbox method.
-s _SORTED, --chrsorted _SORTED //sorted by chromosome size or not, for allotetraploid, it should set to False or F
assigned parameter whether based one genome size [False, True], it's only for Hic matrix of juicerbox method.
-r R, --resolution R resolution used when produce Hic matrix. //resolution [BIN]
-l LOG, --log LOG assigned parameter log hic matrix or not. //wether log or not
-i DPI, --Dpi DPI assigned distinguishability of plot figue,default:300 //dpi
-z FIGS, --figSize FIGS //Figure size assigned figure size,default:(6,6)
-X AXESL, --AxesLen AXESL //Axes length length of x, y axis ticks.
-w AXESW, --Axeswd AXESW //Axes width width of x, y axis ticks.
-d AXESPD, --AxesPd AXESPD //distance between axes and figure region distance between x, y axis ticks label and plot object.
-S GS, --gstyple GS grid linestyle, '-' or 'solid','--' or 'dashed','-.' //grid type or 'dashdot',':' or 'dotted',none
-C COLO, --gColor COLO //grid color grid color, default: black.
-L WD, --glinewd WD grid linewidth!,defult:1 //grid width
-A AP, --gAlpha AP grid alpha!,defult:1 //grid alpha
-B CBSZ, --cbSize CBSZ //color bar size, default 0.5% percentage of plot ax, default: percentage: 0.5.
-D CBPD, --cbPad CBPD //distantance between colorbar and plot ax distantance between colorbar and plot ax!,defalt:0.1
-F FZ, --fontsize FZ fontsize for chromosome when plot whole genome. //fontsize for chromosome
-o FG, --output FG output name of figure //output figure
-R ODIR, --outdir ODIR //outputdir output directory storing result
-v, --verbose show version of kit