7. Provide basic functions to visualize and handle Hi-C data

$ h1d basic
usage: __main__.py basic [-h] [-o OUTNAME] [-c CONTROLMATRIX]
                         [--datatype DATATYPE] [--gt GT] [--plottype PLOTTYPE]
                         [-s START] [-e END] [--normalize NORMALIZE]
                         mode data resolution chromosome

mode, Running mode,,should be one of {plot,dump}
data, Path of matrix file or raw .hic file.
resolution, resolution (50000, i.e.) of given contact matrix, or choosed resolution for analyzing .hic file.
chromosome, selected chromosome to be analyzed.
--datatype, type of input data: “matrix” (default) or “rawhic”.
--gt, genome table file when using raw .hic data.
-o, output name, default: unname

7.1 Plot indicated region

This function provide basic visualization for Hi-C data.

--plottype, Type of plot, could be one of {tri,square,tad}
-s, start site for plot.
-e, end site for plot.
-c, File of control sample. If provided, it will plot differential matrix of treat_vs_control.

h1d basic plot ./test_data/GSE104334_Ctrl.chr21.matrix.gz \
	50000 chr21 --datatype matrix -o testplot --plottype square \
	-s 27500000 -e 32500000

If use --plottype tri:

Differential matrix is plotted when the control data is provided:

h1d basic plot ./test_data/GSE104334_Ctrl.chr21.matrix.gz \
	50000 chr21 --datatype matrix -o testplot --plottype square \
	-s 27500000 -e 32500000

7.2 Make contact matrix.

--normalize, Normalize methods {NONE/VC/VC_SQRT/KR}

h1d basic dump ./test_data/GSE104334_Ctrl.hic 50000 chr21 \
	--datatype rawhic -o testdump --gt ./test_data/hg19_genome_table.txt
	--normalize KR

The output will be:

testdump
└── 50000
    └── observed.KR.chr21.matrix.gz

which is dense matrix (zipped) of intra-chromosomal contacts, like:

	0	25000	50000	75000	...
0	0	0	0	0	...
25000	0	8	3	5	...
50000	0	3	8	4	...
75000	0	5	4	0	...
...	...	...	...	...	...

Dump all chromosomes

chromosome , set chromosome to “all” will compute metrics for all chromosomes.
data, must be .hic data
-maxchr, Maximum index of chromosome (human genome is 22,i.e.). It will compute chromosome 1~maxchr plus chromosome X.
-n, Number of processors

h1d basic dump ./test_data/GSE104334_Ctrl.hic 50000 all \
	--gt ./test_data/hg19_genome_table.txt --normalize KR -o justtest \
	--datatype rawhic --maxchr 22 -n 30

Output would be:

justtest
└── 50000
    ├── observed.KR.chr1.matrix.gz
    ├── observed.KR.chr10.matrix.gz
    ├── observed.KR.chr11.matrix.gz
    ├── observed.KR.chr12.matrix.gz
    ├── observed.KR.chr13.matrix.gz
    ├── observed.KR.chr14.matrix.gz
    ├── observed.KR.chr15.matrix.gz
    ├── observed.KR.chr16.matrix.gz
    ├── observed.KR.chr17.matrix.gz
    ├── observed.KR.chr18.matrix.gz
    ├── observed.KR.chr19.matrix.gz
    ├── observed.KR.chr2.matrix.gz
    ├── observed.KR.chr20.matrix.gz
    ├── observed.KR.chr21.matrix.gz
    ├── observed.KR.chr22.matrix.gz
    ├── observed.KR.chr3.matrix.gz
    ├── observed.KR.chr4.matrix.gz
    ├── observed.KR.chr5.matrix.gz
    ├── observed.KR.chr6.matrix.gz
    ├── observed.KR.chr7.matrix.gz
    ├── observed.KR.chr8.matrix.gz
    ├── observed.KR.chr9.matrix.gz
    └── observed.KR.chrX.matrix.gz

7.3 Make gene density file for PC1

h1d basic gd refFlat.hg19.txt 50000 \
		./test_data/hg19_genome_table.txt -o hg19.geneDensity.txt

refFlat.hg19.txt is defined by UCSC and should be at least 6 columns as (The first column geneName must not be NA):

geneName	name	chrom	strand	txStart	txEnd
RCAN1	NM_001034679	chr1	+	327876	339078
KCNE1	NM_001077977	chr1	+	377375	383871
...	...	..	...	...	...

50000 is the resolution for PC1 analysis.
./test_data/hg19_genome_table.txt is genome table file (tab-separated) which described the length of each chromosome for your genome reference:

chr1	248956422
chr2	242193529
...	...

-o is the output name