hicPlotSVL

Description

hicPlotSVL computes the ratio between short range and long range contacts per chromosome independently. Per sample one box plot is created and, if more than one sample is given, the computed ratios are assumed to be one distribution and a Wilcoxon rank-sum test under H0 ‘distributions are equal’ is computed. All used data is written to a third raw data file.

The distance to distinct short and long range contacts can be set via the –distance parameter; for short range the sum for all contacts smaller or equal this distance are computed, for long range contacts all contacts greater this distance.

Usage example

$ hicPlotSVL -m hmec_10kb.cool nhek_10kb.cool hmec_10kb.cool --distance 2000000 --threads 4 --plotFileName plot.png --outFileName pvalues.txt --outFileNameData rawData.txt

This results in three files:

The raw data containing the sums for short range, long range and ratio per sample and chromosome.

# Created with HiCExplorer's hicPlotSVL 3.3
# Short range vs long range contacts per chromosome: raw data
# Short range contacts: <= 2000000
#   hmec_10kb.cool                  nhek_10kb.cool                  hmec_10kb.cool
# Chromosome        Ratio   Sum <= 2000000  Sum > 2000000   Ratio   Sum <= 2000000  Sum > 2000000   Ratio   Sum <= 2000000  Sum > 2000000
1   3.0399769346724543      33476834        11012200        2.79740105237572        44262902        15822866        3.0399769346724543      33476834        11012200
2   2.7532203542810625      31723954        11522490        2.5007877714355438      47468438        18981394        2.7532203542810625      31723954        11522490
3   2.922650759458664       26251027        8981924 2.6235211241878442      39640848        15109788        2.922650759458664       26251027        8981924
4   2.7235598858451637      22474680        8251950 2.5572455199457864      37486882        14659086        2.7235598858451637      22474680        8251950
5   2.9585962905193712      22716268        7678056 2.752922527526723       35445722        12875670        2.9585962905193712      22716268        7678056
6   3.168274165465025       22872690        7219290 2.8602111006131703      33990211        11883812        3.168274165465025       22872690        7219290
7   3.1093346580597516      19603416        6304698 2.8021236966788887      29712823        10603680        3.1093346580597516      19603416        6304698
8   3.135391026076832       18355087        5854162 2.7964394470859024      28660624        10248970        3.135391026076832       18355087        5854162
9   4.1147978383348125      15395763        3741560 3.819940066283481       21994046        5757694 4.1147978383348125      15395763        3741560
10  3.448063050802953       17964043        5209894 3.1116673856502253      26270171        8442474 3.448063050802953       17964043        5209894
11  3.5924666993070407      18651850        5191934 3.1364875011923035      26240350        8366158 3.5924666993070407      18651850        5191934
12  3.6817551043464416      18640866        5063038 3.306662109403207       26101554        7893626 3.6817551043464416      18640866        5063038
13  3.476204237522881       11018462        3169682 3.0976674036654805      18922281        6108558 3.476204237522881       11018462        3169682
14  3.70550850832778        11164875        3013048 3.6226817463785164      17245704        4760480 3.70550850832778        11164875        3013048
15  4.607631079612186       11165313        2423222 4.567998349104569       15273742        3343640 4.607631079612186       11165313        2423222
16  4.397874357146307       10745775        2443402 3.890983210350018       14666462        3769346 4.397874357146307       10745775        2443402
17  5.809374740402161       12168235        2094586 5.3360710927739285      14154110        2652534 5.809374740402161       12168235        2094586
18  3.7647349280938895      9339833 2480874 3.485487446356812       15019063        4309028 3.7647349280938895      9339833 2480874
19  6.492239632778196       8466283 1304062 5.774337450385819       9368978 1622520 6.492239632778196       8466283 1304062
20  5.542933774973686       8962935 1617002 4.977679877778358       12009479        2412666 5.542933774973686       8962935 1617002
21  6.665622315255486       3910374 586648  6.1843701763589225      6554715 1059884 6.665622315255486       3910374 586648
22  8.063663557923096       4992327 619114  7.433759425439728       5932928 798106  8.063663557923096       4992327 619114
X   2.208752982178897       14424173        6530460 2.3130534357407995      27628734        11944702        2.208752982178897       14424173        6530460
Y   4.165021803993573       36294   8714    3.8063291139240505      45105   11850   4.165021803993573       36294   8714
MT

The p-values between the samples:

# Created with HiCExplorer's hicPlotSVL 3.3
# Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
# Short range contacts: <= 2000000
hmec_10kb.cool      nhek_10kb.cool  0.28362036331636575
hmec_10kb.cool      hmec_10kb.cool  1.0
nhek_10kb.cool      hmec_10kb.cool  0.28362036331636575

The box plot:

../../_images/plot_svl.png